Starting phenix.real_space_refine on Thu Feb 15 04:25:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnt_10536/02_2024/6tnt_10536.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnt_10536/02_2024/6tnt_10536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnt_10536/02_2024/6tnt_10536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnt_10536/02_2024/6tnt_10536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnt_10536/02_2024/6tnt_10536.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnt_10536/02_2024/6tnt_10536.pdb" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 392 5.16 5 C 40893 2.51 5 N 10903 2.21 5 O 11636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 85": "OE1" <-> "OE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1018": "OD1" <-> "OD2" Residue "A PHE 1137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 478": "OE1" <-> "OE2" Residue "C TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 545": "OE1" <-> "OE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "F PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 259": "OE1" <-> "OE2" Residue "J TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 126": "OD1" <-> "OD2" Residue "L PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 342": "OE1" <-> "OE2" Residue "N PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 411": "OD1" <-> "OD2" Residue "N TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 794": "OE1" <-> "OE2" Residue "N TYR 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 226": "OD1" <-> "OD2" Residue "O ASP 266": "OD1" <-> "OD2" Residue "O PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 649": "OE1" <-> "OE2" Residue "O TYR 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 63827 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 11990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1583, 11990 Classifications: {'peptide': 1583} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'CIS': 8, 'PCIS': 3, 'PTRANS': 86, 'TRANS': 1485} Chain breaks: 15 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 14, 'ASP:plan': 18, 'PHE:plan': 1, 'GLU:plan': 30, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 322 Chain: "B" Number of atoms: 649 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 84, 644 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 84, 644 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 660 Chain: "C" Number of atoms: 4306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4306 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 508} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 450 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3618 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 14, 'TRANS': 445} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 220 Classifications: {'peptide': 25} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 21} Chain: "H" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3879 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 473} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "I" Number of atoms: 5634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5634 Classifications: {'peptide': 723} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 696} Chain breaks: 2 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 12, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 124 Chain: "J" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4053 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 489} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "K" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3988 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1435 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 168} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 481 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 5313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5313 Classifications: {'peptide': 672} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 27, 'TRANS': 633} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 263 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 17, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 146 Chain: "O" Number of atoms: 5400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5400 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 669} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'HIS:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "P" Number of atoms: 4046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 4046 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 478} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 79 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'TRANS': 12} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 218 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3767 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "Y" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3862 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 480} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12165 SG CYS B 23 142.422 50.495 104.432 1.00366.90 S ATOM 12356 SG CYS B 51 135.933 43.396 96.320 1.00404.47 S ATOM 12537 SG CYS B 73 135.947 47.045 98.269 1.00398.74 S ATOM 12558 SG CYS B 76 135.476 46.851 94.474 1.00397.40 S Time building chain proxies: 24.99, per 1000 atoms: 0.39 Number of scatterers: 63827 At special positions: 0 Unit cell: (238.7, 175.77, 221.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 392 16.00 O 11636 8.00 N 10903 7.00 C 40893 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.53 Conformation dependent library (CDL) restraints added in 8.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 23 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 51 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 76 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 73 " pdb=" ZN B 103 " pdb="ZN ZN B 103 " - pdb=" NE2 HIS B 58 " 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15526 Finding SS restraints... Secondary structure from input PDB file: 395 helices and 24 sheets defined 70.4% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.83 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 removed outlier: 3.716A pdb=" N ASP A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N HIS A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 630 through 647 Processing helix chain 'A' and resid 655 through 668 Processing helix chain 'A' and resid 705 through 713 Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 724 through 728 removed outlier: 3.826A pdb=" N SER A 727 " --> pdb=" O LEU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 777 removed outlier: 3.679A pdb=" N ILE A 762 " --> pdb=" O HIS A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 798 removed outlier: 3.572A pdb=" N ASP A 796 " --> pdb=" O GLN A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 810 Processing helix chain 'A' and resid 811 through 814 removed outlier: 3.798A pdb=" N VAL A 814 " --> pdb=" O PRO A 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 814' Processing helix chain 'A' and resid 843 through 854 Processing helix chain 'A' and resid 867 through 881 Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 940 through 945 Processing helix chain 'A' and resid 948 through 965 Proline residue: A 954 - end of helix Processing helix chain 'A' and resid 971 through 978 Processing helix chain 'A' and resid 980 through 992 Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1033 through 1042 Processing helix chain 'A' and resid 1058 through 1078 removed outlier: 3.728A pdb=" N GLU A1065 " --> pdb=" O GLU A1061 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG A1076 " --> pdb=" O GLN A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.297A pdb=" N GLY A1083 " --> pdb=" O ALA A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1146 Processing helix chain 'A' and resid 1149 through 1154 removed outlier: 4.136A pdb=" N ASP A1154 " --> pdb=" O ALA A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1183 Processing helix chain 'A' and resid 1183 through 1188 removed outlier: 3.752A pdb=" N LYS A1187 " --> pdb=" O GLY A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1193 through 1200 removed outlier: 4.116A pdb=" N LEU A1197 " --> pdb=" O ILE A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1217 Processing helix chain 'A' and resid 1221 through 1232 Processing helix chain 'A' and resid 1246 through 1261 Processing helix chain 'A' and resid 1266 through 1278 removed outlier: 4.383A pdb=" N GLY A1278 " --> pdb=" O LEU A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1307 removed outlier: 3.752A pdb=" N TYR A1294 " --> pdb=" O ASP A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1331 Processing helix chain 'A' and resid 1359 through 1375 removed outlier: 4.067A pdb=" N THR A1363 " --> pdb=" O ASN A1359 " (cutoff:3.500A) Proline residue: A1365 - end of helix Processing helix chain 'A' and resid 1380 through 1387 Processing helix chain 'A' and resid 1394 through 1399 Processing helix chain 'A' and resid 1400 through 1415 Processing helix chain 'A' and resid 1422 through 1428 Processing helix chain 'A' and resid 1431 through 1437 Processing helix chain 'A' and resid 1458 through 1476 Processing helix chain 'A' and resid 1481 through 1501 Processing helix chain 'A' and resid 1503 through 1508 removed outlier: 4.059A pdb=" N THR A1507 " --> pdb=" O ASN A1503 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1527 Processing helix chain 'A' and resid 1532 through 1545 Processing helix chain 'A' and resid 1551 through 1566 Processing helix chain 'A' and resid 1566 through 1571 removed outlier: 3.580A pdb=" N GLY A1570 " --> pdb=" O PHE A1566 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A1571 " --> pdb=" O LEU A1567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1566 through 1571' Processing helix chain 'A' and resid 1577 through 1588 Processing helix chain 'A' and resid 1603 through 1612 removed outlier: 3.788A pdb=" N HIS A1608 " --> pdb=" O ALA A1605 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR A1610 " --> pdb=" O ARG A1607 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A1612 " --> pdb=" O LEU A1609 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1661 No H-bonds generated for 'chain 'A' and resid 1659 through 1661' Processing helix chain 'A' and resid 1684 through 1693 Processing helix chain 'A' and resid 1734 through 1736 No H-bonds generated for 'chain 'A' and resid 1734 through 1736' Processing helix chain 'A' and resid 1737 through 1742 removed outlier: 3.689A pdb=" N PHE A1741 " --> pdb=" O THR A1737 " (cutoff:3.500A) Processing helix chain 'A' and resid 1744 through 1755 removed outlier: 4.035A pdb=" N PHE A1750 " --> pdb=" O ALA A1746 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A1752 " --> pdb=" O LEU A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1764 through 1781 Processing helix chain 'A' and resid 1783 through 1785 No H-bonds generated for 'chain 'A' and resid 1783 through 1785' Processing helix chain 'A' and resid 1786 through 1802 Processing helix chain 'A' and resid 1808 through 1821 Processing helix chain 'A' and resid 1823 through 1828 removed outlier: 3.605A pdb=" N HIS A1826 " --> pdb=" O SER A1823 " (cutoff:3.500A) Processing helix chain 'A' and resid 1844 through 1863 Processing helix chain 'A' and resid 1864 through 1873 Processing helix chain 'A' and resid 1881 through 1892 removed outlier: 3.848A pdb=" N CYS A1887 " --> pdb=" O SER A1883 " (cutoff:3.500A) Processing helix chain 'A' and resid 1911 through 1921 Processing helix chain 'A' and resid 1924 through 1932 removed outlier: 3.898A pdb=" N LEU A1928 " --> pdb=" O PRO A1924 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG A1930 " --> pdb=" O ARG A1926 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 48 through 62 removed outlier: 3.730A pdb=" N LEU C 58 " --> pdb=" O TRP C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 96 removed outlier: 5.643A pdb=" N ASP C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ALA C 86 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 106 Processing helix chain 'C' and resid 111 through 137 Processing helix chain 'C' and resid 150 through 164 Processing helix chain 'C' and resid 169 through 182 Processing helix chain 'C' and resid 184 through 199 Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.932A pdb=" N TRP C 206 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 222 Processing helix chain 'C' and resid 227 through 242 Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 262 through 276 Processing helix chain 'C' and resid 278 through 293 Processing helix chain 'C' and resid 299 through 311 Processing helix chain 'C' and resid 312 through 327 Processing helix chain 'C' and resid 330 through 344 Processing helix chain 'C' and resid 346 through 361 Processing helix chain 'C' and resid 366 through 379 removed outlier: 3.660A pdb=" N LEU C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 398 through 413 Processing helix chain 'C' and resid 414 through 429 removed outlier: 4.751A pdb=" N TYR C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR C 421 " --> pdb=" O TYR C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 447 removed outlier: 4.384A pdb=" N LEU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 463 Processing helix chain 'C' and resid 468 through 480 Processing helix chain 'C' and resid 482 through 500 Processing helix chain 'C' and resid 510 through 524 Processing helix chain 'C' and resid 525 through 539 Processing helix chain 'C' and resid 544 through 557 Processing helix chain 'D' and resid 26 through 46 Processing helix chain 'E' and resid 53 through 94 removed outlier: 4.439A pdb=" N GLU E 90 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 104 Processing helix chain 'F' and resid 6 through 18 Processing helix chain 'F' and resid 20 through 35 Processing helix chain 'F' and resid 37 through 52 Processing helix chain 'F' and resid 53 through 63 Processing helix chain 'F' and resid 68 through 82 Processing helix chain 'F' and resid 84 through 93 removed outlier: 3.800A pdb=" N LEU F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 111 Processing helix chain 'F' and resid 113 through 128 Processing helix chain 'F' and resid 130 through 145 Processing helix chain 'F' and resid 149 through 159 Processing helix chain 'F' and resid 163 through 168 Processing helix chain 'F' and resid 456 through 478 removed outlier: 3.783A pdb=" N LEU F 462 " --> pdb=" O ALA F 458 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS F 471 " --> pdb=" O ARG F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 490 removed outlier: 3.731A pdb=" N ASN F 486 " --> pdb=" O LYS F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 497 Processing helix chain 'F' and resid 498 through 512 Processing helix chain 'F' and resid 514 through 529 removed outlier: 3.612A pdb=" N ARG F 520 " --> pdb=" O MET F 516 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG F 527 " --> pdb=" O SER F 523 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE F 528 " --> pdb=" O GLU F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 546 removed outlier: 4.175A pdb=" N TYR F 539 " --> pdb=" O GLY F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 563 removed outlier: 4.069A pdb=" N ASP F 561 " --> pdb=" O LYS F 557 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET F 562 " --> pdb=" O ASP F 558 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP F 563 " --> pdb=" O LEU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 580 removed outlier: 3.624A pdb=" N TRP F 570 " --> pdb=" O SER F 566 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLN F 580 " --> pdb=" O CYS F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 597 Processing helix chain 'F' and resid 600 through 614 removed outlier: 4.559A pdb=" N TYR F 604 " --> pdb=" O TYR F 600 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR F 605 " --> pdb=" O ALA F 601 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR F 614 " --> pdb=" O GLU F 610 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 631 Processing helix chain 'F' and resid 634 through 648 Processing helix chain 'F' and resid 650 through 665 removed outlier: 3.757A pdb=" N MET F 656 " --> pdb=" O SER F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 668 through 681 removed outlier: 3.615A pdb=" N LEU F 672 " --> pdb=" O SER F 668 " (cutoff:3.500A) Processing helix chain 'F' and resid 693 through 702 Proline residue: F 700 - end of helix Processing helix chain 'F' and resid 702 through 716 removed outlier: 3.898A pdb=" N LYS F 706 " --> pdb=" O ASN F 702 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN F 716 " --> pdb=" O VAL F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 733 removed outlier: 3.534A pdb=" N ILE F 732 " --> pdb=" O GLU F 728 " (cutoff:3.500A) Processing helix chain 'F' and resid 736 through 749 removed outlier: 3.560A pdb=" N TYR F 740 " --> pdb=" O GLU F 736 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY F 744 " --> pdb=" O TYR F 740 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS F 745 " --> pdb=" O PHE F 741 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL F 746 " --> pdb=" O LEU F 742 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 23 removed outlier: 3.642A pdb=" N GLU G 18 " --> pdb=" O ASP G 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 18 Processing helix chain 'H' and resid 20 through 36 Processing helix chain 'H' and resid 37 through 51 Processing helix chain 'H' and resid 53 through 64 Processing helix chain 'H' and resid 68 through 82 Processing helix chain 'H' and resid 84 through 94 Processing helix chain 'H' and resid 102 through 111 Processing helix chain 'H' and resid 113 through 129 Processing helix chain 'H' and resid 130 through 145 Processing helix chain 'H' and resid 148 through 158 removed outlier: 4.287A pdb=" N PHE H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 174 removed outlier: 4.328A pdb=" N PHE H 168 " --> pdb=" O PRO H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 479 removed outlier: 4.418A pdb=" N GLY H 461 " --> pdb=" O ALA H 457 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU H 462 " --> pdb=" O ALA H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 489 Processing helix chain 'H' and resid 493 through 498 Processing helix chain 'H' and resid 498 through 513 Processing helix chain 'H' and resid 514 through 529 Processing helix chain 'H' and resid 535 through 547 Processing helix chain 'H' and resid 548 through 563 Processing helix chain 'H' and resid 566 through 580 removed outlier: 4.070A pdb=" N TRP H 570 " --> pdb=" O SER H 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 597 Processing helix chain 'H' and resid 600 through 614 removed outlier: 3.734A pdb=" N TYR H 604 " --> pdb=" O TYR H 600 " (cutoff:3.500A) Processing helix chain 'H' and resid 616 through 631 removed outlier: 4.195A pdb=" N ALA H 622 " --> pdb=" O ASP H 618 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS H 623 " --> pdb=" O LYS H 619 " (cutoff:3.500A) Processing helix chain 'H' and resid 634 through 648 removed outlier: 3.726A pdb=" N TRP H 638 " --> pdb=" O HIS H 634 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 665 Processing helix chain 'H' and resid 668 through 682 Processing helix chain 'H' and resid 684 through 699 Processing helix chain 'H' and resid 702 through 717 removed outlier: 3.733A pdb=" N LYS H 706 " --> pdb=" O ASN H 702 " (cutoff:3.500A) Processing helix chain 'H' and resid 718 through 733 Processing helix chain 'H' and resid 736 through 751 removed outlier: 3.716A pdb=" N TYR H 740 " --> pdb=" O GLU H 736 " (cutoff:3.500A) Processing helix chain 'H' and resid 752 through 767 Processing helix chain 'I' and resid 49 through 52 Processing helix chain 'I' and resid 122 through 139 removed outlier: 3.639A pdb=" N LEU I 138 " --> pdb=" O GLU I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 169 Processing helix chain 'I' and resid 238 through 295 Proline residue: I 246 - end of helix removed outlier: 4.417A pdb=" N PHE I 290 " --> pdb=" O ARG I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 310 Processing helix chain 'I' and resid 316 through 325 Processing helix chain 'I' and resid 326 through 372 Processing helix chain 'I' and resid 372 through 377 Processing helix chain 'I' and resid 382 through 429 Processing helix chain 'I' and resid 441 through 451 Processing helix chain 'I' and resid 452 through 457 Processing helix chain 'I' and resid 474 through 480 removed outlier: 3.776A pdb=" N TYR I 478 " --> pdb=" O ARG I 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 503 Processing helix chain 'I' and resid 506 through 510 Processing helix chain 'I' and resid 521 through 548 removed outlier: 3.805A pdb=" N CYS I 536 " --> pdb=" O ILE I 532 " (cutoff:3.500A) Proline residue: I 540 - end of helix removed outlier: 3.599A pdb=" N MET I 548 " --> pdb=" O ILE I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 671 through 675 Processing helix chain 'I' and resid 692 through 696 Processing helix chain 'J' and resid 3 through 17 Processing helix chain 'J' and resid 18 through 34 Processing helix chain 'J' and resid 36 through 50 Processing helix chain 'J' and resid 52 through 62 Processing helix chain 'J' and resid 64 through 70 removed outlier: 3.876A pdb=" N LEU J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 83 removed outlier: 3.807A pdb=" N LEU J 75 " --> pdb=" O ALA J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 94 Processing helix chain 'J' and resid 125 through 143 Processing helix chain 'J' and resid 145 through 160 Processing helix chain 'J' and resid 164 through 173 Processing helix chain 'J' and resid 177 through 188 Processing helix chain 'J' and resid 194 through 208 Processing helix chain 'J' and resid 224 through 230 removed outlier: 4.027A pdb=" N GLU J 229 " --> pdb=" O ASP J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 230 through 245 Processing helix chain 'J' and resid 246 through 261 removed outlier: 4.084A pdb=" N VAL J 256 " --> pdb=" O LYS J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 279 Processing helix chain 'J' and resid 280 through 295 Processing helix chain 'J' and resid 298 through 313 removed outlier: 4.196A pdb=" N TRP J 302 " --> pdb=" O ASN J 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 330 Processing helix chain 'J' and resid 333 through 347 removed outlier: 3.614A pdb=" N TRP J 337 " --> pdb=" O TYR J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 364 Processing helix chain 'J' and resid 368 through 381 Processing helix chain 'J' and resid 383 through 397 Processing helix chain 'J' and resid 401 through 416 Processing helix chain 'J' and resid 418 through 433 Processing helix chain 'J' and resid 444 through 458 Processing helix chain 'J' and resid 460 through 475 Processing helix chain 'J' and resid 478 through 492 Processing helix chain 'J' and resid 494 through 509 Processing helix chain 'J' and resid 512 through 529 removed outlier: 3.739A pdb=" N VAL J 516 " --> pdb=" O ASP J 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 17 Processing helix chain 'K' and resid 18 through 34 Processing helix chain 'K' and resid 36 through 50 Processing helix chain 'K' and resid 52 through 62 Processing helix chain 'K' and resid 64 through 69 Processing helix chain 'K' and resid 69 through 83 Processing helix chain 'K' and resid 88 through 93 Processing helix chain 'K' and resid 128 through 143 removed outlier: 3.790A pdb=" N GLY K 137 " --> pdb=" O CYS K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 160 removed outlier: 4.333A pdb=" N TYR K 151 " --> pdb=" O THR K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 172 removed outlier: 3.858A pdb=" N PHE K 167 " --> pdb=" O CYS K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 178 removed outlier: 3.615A pdb=" N ALA K 178 " --> pdb=" O MET K 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 175 through 178' Processing helix chain 'K' and resid 179 through 188 Processing helix chain 'K' and resid 194 through 210 removed outlier: 3.635A pdb=" N GLU K 199 " --> pdb=" O ASN K 195 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG K 202 " --> pdb=" O GLN K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 225 removed outlier: 4.231A pdb=" N VAL K 224 " --> pdb=" O ILE K 220 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 229 Processing helix chain 'K' and resid 230 through 244 removed outlier: 3.503A pdb=" N VAL K 234 " --> pdb=" O ASN K 230 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU K 237 " --> pdb=" O VAL K 233 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG K 240 " --> pdb=" O SER K 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 261 Processing helix chain 'K' and resid 267 through 278 removed outlier: 4.150A pdb=" N GLY K 273 " --> pdb=" O PRO K 269 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU K 277 " --> pdb=" O GLY K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 295 Processing helix chain 'K' and resid 298 through 313 removed outlier: 3.985A pdb=" N TRP K 302 " --> pdb=" O ASN K 298 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR K 309 " --> pdb=" O VAL K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 330 removed outlier: 3.815A pdb=" N ARG K 321 " --> pdb=" O GLU K 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 333 through 346 removed outlier: 4.054A pdb=" N TRP K 337 " --> pdb=" O TYR K 333 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE K 338 " --> pdb=" O GLY K 334 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE K 344 " --> pdb=" O TYR K 340 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 362 removed outlier: 3.733A pdb=" N MET K 354 " --> pdb=" O HIS K 350 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA K 355 " --> pdb=" O ASP K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 381 removed outlier: 4.474A pdb=" N MET K 371 " --> pdb=" O CYS K 367 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY K 375 " --> pdb=" O MET K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 398 removed outlier: 3.558A pdb=" N ILE K 397 " --> pdb=" O GLN K 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 401 through 416 Processing helix chain 'K' and resid 417 through 435 removed outlier: 3.987A pdb=" N LYS K 423 " --> pdb=" O LYS K 419 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS K 431 " --> pdb=" O ASP K 427 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA K 434 " --> pdb=" O GLU K 430 " (cutoff:3.500A) Processing helix chain 'K' and resid 441 through 444 Processing helix chain 'K' and resid 445 through 458 removed outlier: 3.587A pdb=" N ASN K 449 " --> pdb=" O GLU K 445 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL K 454 " --> pdb=" O ASN K 450 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 475 removed outlier: 3.684A pdb=" N GLN K 470 " --> pdb=" O ASP K 466 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL K 473 " --> pdb=" O ARG K 469 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU K 474 " --> pdb=" O GLN K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 492 removed outlier: 3.534A pdb=" N ALA K 484 " --> pdb=" O SER K 480 " (cutoff:3.500A) Processing helix chain 'K' and resid 494 through 509 removed outlier: 3.534A pdb=" N VAL K 499 " --> pdb=" O PHE K 495 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR K 504 " --> pdb=" O ASP K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 512 through 527 Processing helix chain 'L' and resid 12 through 20 removed outlier: 3.926A pdb=" N GLY L 20 " --> pdb=" O LEU L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 Processing helix chain 'L' and resid 144 through 148 removed outlier: 4.013A pdb=" N ASN L 147 " --> pdb=" O ASN L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 179 Processing helix chain 'M' and resid 8 through 16 removed outlier: 4.431A pdb=" N ASP M 16 " --> pdb=" O LEU M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 22 Processing helix chain 'M' and resid 49 through 56 Processing helix chain 'N' and resid 16 through 30 Processing helix chain 'N' and resid 51 through 64 Processing helix chain 'N' and resid 69 through 101 removed outlier: 4.520A pdb=" N GLU N 73 " --> pdb=" O SER N 69 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER N 88 " --> pdb=" O GLN N 84 " (cutoff:3.500A) Proline residue: N 89 - end of helix removed outlier: 3.541A pdb=" N SER N 101 " --> pdb=" O GLN N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 121 Processing helix chain 'N' and resid 122 through 138 removed outlier: 3.989A pdb=" N LEU N 126 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS N 134 " --> pdb=" O GLU N 130 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU N 138 " --> pdb=" O LYS N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 162 removed outlier: 4.959A pdb=" N VAL N 153 " --> pdb=" O LEU N 149 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N HIS N 154 " --> pdb=" O ARG N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 191 removed outlier: 3.613A pdb=" N GLU N 171 " --> pdb=" O ARG N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 233 through 250 Processing helix chain 'N' and resid 252 through 278 removed outlier: 4.784A pdb=" N GLU N 259 " --> pdb=" O ARG N 255 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA N 260 " --> pdb=" O VAL N 256 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR N 263 " --> pdb=" O GLU N 259 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG N 276 " --> pdb=" O ARG N 272 " (cutoff:3.500A) Processing helix chain 'N' and resid 290 through 304 Processing helix chain 'N' and resid 321 through 343 Processing helix chain 'N' and resid 343 through 350 Processing helix chain 'N' and resid 354 through 368 Processing helix chain 'N' and resid 371 through 387 Processing helix chain 'N' and resid 392 through 407 Processing helix chain 'N' and resid 413 through 431 removed outlier: 4.468A pdb=" N LEU N 417 " --> pdb=" O SER N 413 " (cutoff:3.500A) Proline residue: N 423 - end of helix Processing helix chain 'N' and resid 434 through 443 Processing helix chain 'N' and resid 500 through 509 removed outlier: 4.151A pdb=" N LEU N 504 " --> pdb=" O ASP N 500 " (cutoff:3.500A) Processing helix chain 'N' and resid 511 through 527 Processing helix chain 'N' and resid 534 through 549 Processing helix chain 'N' and resid 551 through 580 removed outlier: 4.083A pdb=" N VAL N 559 " --> pdb=" O HIS N 555 " (cutoff:3.500A) Processing helix chain 'N' and resid 612 through 630 removed outlier: 3.987A pdb=" N ALA N 617 " --> pdb=" O GLU N 613 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA N 618 " --> pdb=" O ASP N 614 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 642 removed outlier: 3.875A pdb=" N LEU N 641 " --> pdb=" O LYS N 638 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY N 642 " --> pdb=" O HIS N 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 638 through 642' Processing helix chain 'N' and resid 660 through 672 removed outlier: 4.554A pdb=" N ILE N 666 " --> pdb=" O VAL N 662 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU N 667 " --> pdb=" O GLN N 663 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP N 672 " --> pdb=" O LEU N 668 " (cutoff:3.500A) Processing helix chain 'N' and resid 677 through 686 Processing helix chain 'N' and resid 688 through 703 Processing helix chain 'N' and resid 751 through 764 removed outlier: 3.594A pdb=" N THR N 756 " --> pdb=" O LEU N 752 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR N 757 " --> pdb=" O LEU N 753 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE N 758 " --> pdb=" O PHE N 754 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN N 759 " --> pdb=" O TRP N 755 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN N 764 " --> pdb=" O ALA N 760 " (cutoff:3.500A) Processing helix chain 'N' and resid 771 through 782 removed outlier: 4.041A pdb=" N VAL N 782 " --> pdb=" O ARG N 778 " (cutoff:3.500A) Processing helix chain 'N' and resid 792 through 806 Processing helix chain 'O' and resid 31 through 45 Processing helix chain 'O' and resid 53 through 70 removed outlier: 4.325A pdb=" N LEU O 65 " --> pdb=" O ASN O 61 " (cutoff:3.500A) Proline residue: O 66 - end of helix Processing helix chain 'O' and resid 74 through 84 Processing helix chain 'O' and resid 86 through 103 removed outlier: 3.719A pdb=" N ALA O 90 " --> pdb=" O CYS O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 121 removed outlier: 3.925A pdb=" N MET O 108 " --> pdb=" O GLU O 104 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER O 120 " --> pdb=" O SER O 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 146 Processing helix chain 'O' and resid 147 through 167 Processing helix chain 'O' and resid 208 through 225 Processing helix chain 'O' and resid 232 through 247 Processing helix chain 'O' and resid 251 through 265 Processing helix chain 'O' and resid 267 through 281 Processing helix chain 'O' and resid 298 through 315 removed outlier: 4.003A pdb=" N TYR O 302 " --> pdb=" O ARG O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 316 through 334 Processing helix chain 'O' and resid 337 through 351 Processing helix chain 'O' and resid 360 through 370 removed outlier: 3.624A pdb=" N SER O 364 " --> pdb=" O LEU O 360 " (cutoff:3.500A) Processing helix chain 'O' and resid 373 through 391 Processing helix chain 'O' and resid 402 through 413 removed outlier: 3.520A pdb=" N HIS O 412 " --> pdb=" O LEU O 408 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 432 Processing helix chain 'O' and resid 434 through 448 Processing helix chain 'O' and resid 463 through 480 Processing helix chain 'O' and resid 482 through 497 Processing helix chain 'O' and resid 503 through 523 Processing helix chain 'O' and resid 524 through 539 removed outlier: 3.720A pdb=" N THR O 533 " --> pdb=" O ASP O 529 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY O 534 " --> pdb=" O SER O 530 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 554 Processing helix chain 'O' and resid 556 through 575 Processing helix chain 'O' and resid 576 through 592 Processing helix chain 'O' and resid 596 through 598 No H-bonds generated for 'chain 'O' and resid 596 through 598' Processing helix chain 'O' and resid 599 through 615 removed outlier: 4.680A pdb=" N MET O 603 " --> pdb=" O ILE O 599 " (cutoff:3.500A) Processing helix chain 'O' and resid 616 through 635 Processing helix chain 'O' and resid 636 through 654 removed outlier: 3.840A pdb=" N MET O 646 " --> pdb=" O SER O 642 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA O 647 " --> pdb=" O LEU O 643 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLU O 649 " --> pdb=" O HIS O 645 " (cutoff:3.500A) Proline residue: O 650 - end of helix Processing helix chain 'O' and resid 657 through 676 Processing helix chain 'O' and resid 682 through 705 Processing helix chain 'O' and resid 707 through 725 removed outlier: 3.922A pdb=" N ASP O 712 " --> pdb=" O GLU O 708 " (cutoff:3.500A) Processing helix chain 'O' and resid 726 through 742 removed outlier: 3.775A pdb=" N LEU O 736 " --> pdb=" O ARG O 732 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 47 Processing helix chain 'P' and resid 48 through 62 Processing helix chain 'P' and resid 77 through 97 removed outlier: 4.857A pdb=" N ASP P 85 " --> pdb=" O ALA P 81 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA P 86 " --> pdb=" O GLN P 82 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU P 89 " --> pdb=" O ASP P 85 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS P 97 " --> pdb=" O TYR P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 107 Processing helix chain 'P' and resid 111 through 134 Processing helix chain 'P' and resid 148 through 164 removed outlier: 4.243A pdb=" N LEU P 154 " --> pdb=" O ALA P 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 182 removed outlier: 3.503A pdb=" N TYR P 173 " --> pdb=" O GLY P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 199 removed outlier: 4.000A pdb=" N ASP P 190 " --> pdb=" O LYS P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 211 removed outlier: 3.711A pdb=" N TRP P 206 " --> pdb=" O HIS P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 215 through 221 Processing helix chain 'P' and resid 228 through 241 removed outlier: 4.145A pdb=" N PHE P 232 " --> pdb=" O TRP P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 258 removed outlier: 3.640A pdb=" N ALA P 247 " --> pdb=" O LEU P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 262 through 276 removed outlier: 3.742A pdb=" N VAL P 266 " --> pdb=" O SER P 262 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE P 276 " --> pdb=" O ALA P 272 " (cutoff:3.500A) Processing helix chain 'P' and resid 278 through 293 removed outlier: 3.608A pdb=" N ILE P 285 " --> pdb=" O LYS P 281 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU P 288 " --> pdb=" O SER P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 299 through 310 removed outlier: 3.512A pdb=" N PHE P 303 " --> pdb=" O ASN P 299 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL P 309 " --> pdb=" O ASN P 305 " (cutoff:3.500A) Processing helix chain 'P' and resid 312 through 327 removed outlier: 3.931A pdb=" N GLU P 325 " --> pdb=" O HIS P 321 " (cutoff:3.500A) Processing helix chain 'P' and resid 332 through 344 removed outlier: 3.905A pdb=" N GLY P 338 " --> pdb=" O CYS P 334 " (cutoff:3.500A) Processing helix chain 'P' and resid 346 through 358 removed outlier: 3.617A pdb=" N PHE P 354 " --> pdb=" O ALA P 350 " (cutoff:3.500A) Processing helix chain 'P' and resid 364 through 378 removed outlier: 3.971A pdb=" N TRP P 368 " --> pdb=" O TYR P 364 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR P 369 " --> pdb=" O LEU P 365 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET P 371 " --> pdb=" O ALA P 367 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS P 373 " --> pdb=" O THR P 369 " (cutoff:3.500A) Processing helix chain 'P' and resid 380 through 395 removed outlier: 3.642A pdb=" N ALA P 391 " --> pdb=" O ALA P 387 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU P 393 " --> pdb=" O ARG P 389 " (cutoff:3.500A) Processing helix chain 'P' and resid 398 through 412 removed outlier: 3.533A pdb=" N LEU P 405 " --> pdb=" O ALA P 401 " (cutoff:3.500A) Processing helix chain 'P' and resid 414 through 429 removed outlier: 3.927A pdb=" N CYS P 418 " --> pdb=" O MET P 414 " (cutoff:3.500A) Processing helix chain 'P' and resid 432 through 447 Processing helix chain 'P' and resid 448 through 463 Processing helix chain 'P' and resid 468 through 480 removed outlier: 3.954A pdb=" N HIS P 477 " --> pdb=" O LEU P 473 " (cutoff:3.500A) Processing helix chain 'P' and resid 482 through 500 removed outlier: 3.653A pdb=" N ALA P 486 " --> pdb=" O GLU P 482 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP P 496 " --> pdb=" O LYS P 492 " (cutoff:3.500A) Processing helix chain 'P' and resid 512 through 523 removed outlier: 3.777A pdb=" N GLN P 518 " --> pdb=" O ARG P 514 " (cutoff:3.500A) Processing helix chain 'P' and resid 525 through 538 removed outlier: 3.871A pdb=" N CYS P 532 " --> pdb=" O GLU P 528 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS P 535 " --> pdb=" O THR P 531 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA P 538 " --> pdb=" O GLN P 534 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 23 removed outlier: 4.544A pdb=" N GLU W 18 " --> pdb=" O ASP W 14 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE W 19 " --> pdb=" O ASP W 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 48 Processing helix chain 'X' and resid 49 through 67 Processing helix chain 'X' and resid 72 through 90 Processing helix chain 'X' and resid 92 through 110 Processing helix chain 'X' and resid 134 through 150 Processing helix chain 'X' and resid 151 through 161 removed outlier: 3.509A pdb=" N ALA X 155 " --> pdb=" O GLN X 151 " (cutoff:3.500A) Processing helix chain 'X' and resid 163 through 167 Processing helix chain 'X' and resid 168 through 183 Processing helix chain 'X' and resid 184 through 199 Processing helix chain 'X' and resid 202 through 213 Processing helix chain 'X' and resid 214 through 229 removed outlier: 4.429A pdb=" N GLU X 218 " --> pdb=" O VAL X 214 " (cutoff:3.500A) Processing helix chain 'X' and resid 234 through 249 removed outlier: 4.137A pdb=" N VAL X 238 " --> pdb=" O ASP X 234 " (cutoff:3.500A) Processing helix chain 'X' and resid 250 through 264 Processing helix chain 'X' and resid 270 through 285 Processing helix chain 'X' and resid 286 through 301 Processing helix chain 'X' and resid 304 through 319 removed outlier: 4.156A pdb=" N ASP X 309 " --> pdb=" O ILE X 305 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL X 310 " --> pdb=" O LYS X 306 " (cutoff:3.500A) Processing helix chain 'X' and resid 320 through 335 Processing helix chain 'X' and resid 338 through 352 removed outlier: 4.263A pdb=" N TRP X 342 " --> pdb=" O HIS X 338 " (cutoff:3.500A) Processing helix chain 'X' and resid 354 through 369 Processing helix chain 'X' and resid 373 through 387 Processing helix chain 'X' and resid 388 through 403 removed outlier: 3.757A pdb=" N ALA X 392 " --> pdb=" O ARG X 388 " (cutoff:3.500A) Processing helix chain 'X' and resid 407 through 421 Processing helix chain 'X' and resid 422 through 438 Processing helix chain 'X' and resid 441 through 454 removed outlier: 3.521A pdb=" N THR X 445 " --> pdb=" O ALA X 441 " (cutoff:3.500A) Processing helix chain 'X' and resid 457 through 472 removed outlier: 3.908A pdb=" N LEU X 464 " --> pdb=" O LYS X 460 " (cutoff:3.500A) Processing helix chain 'X' and resid 475 through 490 Processing helix chain 'X' and resid 492 through 504 Processing helix chain 'X' and resid 508 through 520 removed outlier: 4.003A pdb=" N HIS X 512 " --> pdb=" O ASP X 508 " (cutoff:3.500A) Processing helix chain 'X' and resid 524 through 539 Processing helix chain 'Y' and resid 37 through 48 Processing helix chain 'Y' and resid 49 through 67 Processing helix chain 'Y' and resid 72 through 91 Processing helix chain 'Y' and resid 92 through 110 Processing helix chain 'Y' and resid 134 through 149 Processing helix chain 'Y' and resid 151 through 162 removed outlier: 3.627A pdb=" N ALA Y 155 " --> pdb=" O GLN Y 151 " (cutoff:3.500A) Processing helix chain 'Y' and resid 168 through 183 Processing helix chain 'Y' and resid 184 through 199 removed outlier: 3.967A pdb=" N CYS Y 199 " --> pdb=" O VAL Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 202 through 213 Processing helix chain 'Y' and resid 214 through 229 Processing helix chain 'Y' and resid 230 through 234 Processing helix chain 'Y' and resid 235 through 249 removed outlier: 3.570A pdb=" N GLY Y 249 " --> pdb=" O PHE Y 245 " (cutoff:3.500A) Processing helix chain 'Y' and resid 250 through 264 removed outlier: 3.787A pdb=" N ALA Y 254 " --> pdb=" O ASP Y 250 " (cutoff:3.500A) Processing helix chain 'Y' and resid 265 through 268 Processing helix chain 'Y' and resid 270 through 285 Processing helix chain 'Y' and resid 286 through 301 Processing helix chain 'Y' and resid 307 through 319 removed outlier: 3.980A pdb=" N TYR Y 313 " --> pdb=" O ASP Y 309 " (cutoff:3.500A) Processing helix chain 'Y' and resid 320 through 335 Processing helix chain 'Y' and resid 338 through 352 removed outlier: 4.297A pdb=" N TRP Y 342 " --> pdb=" O HIS Y 338 " (cutoff:3.500A) Processing helix chain 'Y' and resid 354 through 369 Processing helix chain 'Y' and resid 372 through 387 Processing helix chain 'Y' and resid 388 through 403 Processing helix chain 'Y' and resid 406 through 421 Processing helix chain 'Y' and resid 422 through 438 Processing helix chain 'Y' and resid 441 through 451 Processing helix chain 'Y' and resid 457 through 472 removed outlier: 3.818A pdb=" N LEU Y 464 " --> pdb=" O LYS Y 460 " (cutoff:3.500A) Processing helix chain 'Y' and resid 475 through 490 Processing helix chain 'Y' and resid 492 through 506 removed outlier: 3.940A pdb=" N ASN Y 505 " --> pdb=" O ASN Y 501 " (cutoff:3.500A) Processing helix chain 'Y' and resid 508 through 523 removed outlier: 4.100A pdb=" N HIS Y 512 " --> pdb=" O ASP Y 508 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA Y 521 " --> pdb=" O ASP Y 517 " (cutoff:3.500A) Processing helix chain 'Y' and resid 524 through 539 Processing helix chain 'Y' and resid 542 through 552 removed outlier: 3.748A pdb=" N GLY Y 548 " --> pdb=" O LYS Y 544 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.578A pdb=" N ILE A 12 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 509 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU A 497 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP A 478 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 3.653A pdb=" N GLN A 18 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG A 594 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP A 589 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR A 596 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE A 587 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLU A 598 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 78 Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.590A pdb=" N ILE A 151 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 162 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.852A pdb=" N PHE A 211 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.527A pdb=" N GLN A 237 " --> pdb=" O CYS A 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 245 through 250 removed outlier: 6.676A pdb=" N MET A 257 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU A 249 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 255 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP A 413 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A 270 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N HIS A 411 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 427 through 434 removed outlier: 3.947A pdb=" N LYS A 429 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 440 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 452 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 474 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER A 470 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN A 458 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N PHE A 468 " --> pdb=" O GLN A 458 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1109 through 1111 removed outlier: 3.709A pdb=" N THR A1116 " --> pdb=" O ALA A1111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1352 through 1353 removed outlier: 12.179A pdb=" N ILE L 66 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N ALA L 140 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 11.925A pdb=" N PHE L 68 " --> pdb=" O GLN L 138 " (cutoff:3.500A) removed outlier: 11.461A pdb=" N GLN L 138 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 10.570A pdb=" N ARG L 70 " --> pdb=" O MET L 136 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET L 136 " --> pdb=" O ARG L 70 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL L 98 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLU L 107 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1572 through 1574 Processing sheet with id=AB3, first strand: chain 'A' and resid 1628 through 1629 removed outlier: 3.644A pdb=" N THR A1628 " --> pdb=" O ASP A1623 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A1619 " --> pdb=" O THR A1655 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A1655 " --> pdb=" O LEU A1619 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1628 through 1629 removed outlier: 3.644A pdb=" N THR A1628 " --> pdb=" O ASP A1623 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1647 through 1652 removed outlier: 3.826A pdb=" N THR A1647 " --> pdb=" O TYR A1638 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A1633 " --> pdb=" O VAL A1668 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL A1668 " --> pdb=" O LEU A1633 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU A1635 " --> pdb=" O ILE A1666 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE A1666 " --> pdb=" O GLU A1635 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR A1637 " --> pdb=" O LYS A1664 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 46 through 48 removed outlier: 3.741A pdb=" N VAL B 47 " --> pdb=" O PHE B 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 12 through 15 removed outlier: 5.867A pdb=" N VAL I 13 " --> pdb=" O GLU I 745 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU I 745 " --> pdb=" O VAL I 13 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 23 through 28 removed outlier: 6.553A pdb=" N ALA I 38 " --> pdb=" O ILE I 24 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU I 26 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ALA I 36 " --> pdb=" O LEU I 26 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 68 through 73 removed outlier: 4.448A pdb=" N CYS I 70 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU I 80 " --> pdb=" O CYS I 93 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS I 89 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 113 through 115 removed outlier: 5.731A pdb=" N ALA I 189 " --> pdb=" O LYS I 194 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LYS I 194 " --> pdb=" O ALA I 189 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 205 through 210 removed outlier: 6.219A pdb=" N CYS I 205 " --> pdb=" O GLU I 222 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLU I 222 " --> pdb=" O CYS I 205 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER I 229 " --> pdb=" O ARG I 558 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG I 558 " --> pdb=" O SER I 229 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL I 231 " --> pdb=" O LEU I 556 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 574 through 578 removed outlier: 12.804A pdb=" N TYR I 596 " --> pdb=" O PHE I 620 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N PHE I 620 " --> pdb=" O TYR I 596 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N MET I 598 " --> pdb=" O ILE I 618 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG I 703 " --> pdb=" O ALA I 617 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE I 707 " --> pdb=" O GLY I 621 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE I 623 " --> pdb=" O PHE I 707 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 636 through 643 removed outlier: 6.013A pdb=" N CYS I 638 " --> pdb=" O LYS I 654 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS I 654 " --> pdb=" O CYS I 638 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP I 640 " --> pdb=" O VAL I 652 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 22 through 24 removed outlier: 4.389A pdb=" N GLN L 155 " --> pdb=" O TYR L 80 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 54 through 55 4097 hydrogen bonds defined for protein. 12162 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.82 Time building geometry restraints manager: 22.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 20672 1.34 - 1.46: 13803 1.46 - 1.58: 30124 1.58 - 1.69: 0 1.69 - 1.81: 598 Bond restraints: 65197 Sorted by residual: bond pdb=" CA LEU A1609 " pdb=" C LEU A1609 " ideal model delta sigma weight residual 1.523 1.482 0.042 1.80e-02 3.09e+03 5.37e+00 bond pdb=" N LEU N 122 " pdb=" CA LEU N 122 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.74e+00 bond pdb=" C ARG N 121 " pdb=" N LEU N 122 " ideal model delta sigma weight residual 1.329 1.354 -0.025 1.40e-02 5.10e+03 3.07e+00 bond pdb=" C THR A1641 " pdb=" N GLN A1642 " ideal model delta sigma weight residual 1.333 1.301 0.031 1.92e-02 2.71e+03 2.69e+00 bond pdb=" C ARG N 581 " pdb=" N PRO N 582 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.29e+00 ... (remaining 65192 not shown) Histogram of bond angle deviations from ideal: 99.23 - 107.29: 2170 107.29 - 115.36: 39618 115.36 - 123.42: 44643 123.42 - 131.48: 1792 131.48 - 139.54: 130 Bond angle restraints: 88353 Sorted by residual: angle pdb=" C ARG N 121 " pdb=" N LEU N 122 " pdb=" CA LEU N 122 " ideal model delta sigma weight residual 121.70 139.07 -17.37 1.80e+00 3.09e-01 9.32e+01 angle pdb=" CA ARG N 121 " pdb=" C ARG N 121 " pdb=" N LEU N 122 " ideal model delta sigma weight residual 116.92 125.58 -8.66 1.16e+00 7.43e-01 5.58e+01 angle pdb=" C HIS A 758 " pdb=" N ILE A 759 " pdb=" CA ILE A 759 " ideal model delta sigma weight residual 120.24 124.31 -4.07 6.30e-01 2.52e+00 4.18e+01 angle pdb=" N SER Y 213 " pdb=" CA SER Y 213 " pdb=" C SER Y 213 " ideal model delta sigma weight residual 108.19 116.47 -8.28 1.29e+00 6.01e-01 4.12e+01 angle pdb=" N ARG N 121 " pdb=" CA ARG N 121 " pdb=" C ARG N 121 " ideal model delta sigma weight residual 110.97 117.07 -6.10 1.09e+00 8.42e-01 3.13e+01 ... (remaining 88348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 35728 17.85 - 35.69: 2595 35.69 - 53.54: 742 53.54 - 71.39: 148 71.39 - 89.23: 37 Dihedral angle restraints: 39250 sinusoidal: 15295 harmonic: 23955 Sorted by residual: dihedral pdb=" CA ALA O 656 " pdb=" C ALA O 656 " pdb=" N ILE O 657 " pdb=" CA ILE O 657 " ideal model delta harmonic sigma weight residual 180.00 143.30 36.70 0 5.00e+00 4.00e-02 5.39e+01 dihedral pdb=" CA TRP B 14 " pdb=" C TRP B 14 " pdb=" N LEU B 15 " pdb=" CA LEU B 15 " ideal model delta harmonic sigma weight residual 0.00 -34.14 34.14 0 5.00e+00 4.00e-02 4.66e+01 dihedral pdb=" CA PHE I 451 " pdb=" C PHE I 451 " pdb=" N LEU I 452 " pdb=" CA LEU I 452 " ideal model delta harmonic sigma weight residual -180.00 -146.94 -33.06 0 5.00e+00 4.00e-02 4.37e+01 ... (remaining 39247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 8141 0.050 - 0.099: 1572 0.099 - 0.149: 243 0.149 - 0.198: 3 0.198 - 0.248: 4 Chirality restraints: 9963 Sorted by residual: chirality pdb=" CA ARG N 121 " pdb=" N ARG N 121 " pdb=" C ARG N 121 " pdb=" CB ARG N 121 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB ILE O 581 " pdb=" CA ILE O 581 " pdb=" CG1 ILE O 581 " pdb=" CG2 ILE O 581 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA LEU N 122 " pdb=" N LEU N 122 " pdb=" C LEU N 122 " pdb=" CB LEU N 122 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 9960 not shown) Planarity restraints: 11210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR O 129 " -0.024 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C THR O 129 " 0.084 2.00e-02 2.50e+03 pdb=" O THR O 129 " -0.032 2.00e-02 2.50e+03 pdb=" N SER O 130 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER O 540 " 0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C SER O 540 " -0.062 2.00e-02 2.50e+03 pdb=" O SER O 540 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE O 541 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 102 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C SER H 102 " 0.056 2.00e-02 2.50e+03 pdb=" O SER H 102 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS H 103 " -0.019 2.00e-02 2.50e+03 ... (remaining 11207 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 634 2.54 - 3.13: 53702 3.13 - 3.72: 106949 3.72 - 4.31: 139716 4.31 - 4.90: 228926 Nonbonded interactions: 529927 Sorted by model distance: nonbonded pdb=" CE1 TYR L 89 " pdb=" OD2 ASP L 150 " model vdw 1.949 3.340 nonbonded pdb=" CE1 TYR L 89 " pdb=" OD1 ASP L 150 " model vdw 2.022 3.340 nonbonded pdb=" OH TYR K 309 " pdb=" OD2 ASP M 59 " model vdw 2.063 2.440 nonbonded pdb=" OH TYR F 73 " pdb=" O HIS H 18 " model vdw 2.091 2.440 nonbonded pdb=" O ASN Y 225 " pdb=" OG1 THR Y 229 " model vdw 2.092 2.440 ... (remaining 529922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 26 through 135 or resid 147 through 160 or (resid 161 and \ (name N or name CA or name C or name O or name CB )) or resid 162 through 496 or \ (resid 497 and (name N or name CA or name C or name O or name CB or name CG1 or \ name CG2)) or resid 498 through 500 or resid 511 through 538)) selection = chain 'P' } ncs_group { reference = (chain 'F' and (resid 5 through 167 or (resid 168 through 459 and (name N or nam \ e CA or name C or name O or name CB )) or resid 460 through 755)) selection = (chain 'H' and (resid 5 through 95 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 through 171 or (resid 455 through 459 and ( \ name N or name CA or name C or name O or name CB )) or resid 460 through 461 or \ (resid 462 and (name N or name CA or name C or name O or name CB )) or resid 463 \ through 470 or (resid 471 and (name N or name CA or name C or name O or name CB \ )) or resid 472 through 477 or (resid 478 and (name N or name CA or name C or n \ ame O or name CB )) or resid 479 through 481 or (resid 482 and (name N or name C \ A or name C or name O or name CB )) or resid 483 through 556 or (resid 557 and ( \ name N or name CA or name C or name O or name CB )) or resid 558 through 587 or \ (resid 588 and (name N or name CA or name C or name O or name CB )) or resid 589 \ through 682 or (resid 691 and (name N or name CA or name C or name O or name CB \ )) or resid 692 or (resid 693 through 701 and (name N or name CA or name C or n \ ame O or name CB )) or resid 702 through 705 or (resid 706 and (name N or name C \ A or name C or name O or name CB )) or resid 707 through 719 or (resid 720 and ( \ name N or name CA or name C or name O or name CB )) or resid 721 through 734 or \ (resid 735 and (name N or name CA or name C or name O or name CB )) or resid 736 \ through 737 or (resid 738 and (name N or name CA or name C or name O or name CB \ )) or resid 739 through 747 or (resid 748 and (name N or name CA or name C or n \ ame O or name CB )) or resid 749 through 753 or (resid 754 and (name N or name C \ A or name C or name O or name CB )) or resid 755)) } ncs_group { reference = (chain 'G' and (resid 1 through 23 or (resid 24 through 25 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'W' and resid 1 through 25) } ncs_group { reference = (chain 'J' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 93 or resid 127 through 227 or (resid 228 and (na \ me N or name CA or name C or name O or name CB )) or resid 229 through 527)) selection = (chain 'K' and (resid 2 through 221 or (resid 222 and (name N or name CA or name \ C or name O or name CB )) or resid 223 through 346 or (resid 347 and (name N or \ name CA or name C or name O or name CB )) or resid 348 through 523 or (resid 52 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 525 through \ 527)) } ncs_group { reference = chain 'X' selection = (chain 'Y' and resid 36 through 540) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 10.420 Check model and map are aligned: 0.720 Set scattering table: 0.480 Process input model: 144.090 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 65197 Z= 0.307 Angle : 0.664 17.373 88353 Z= 0.374 Chirality : 0.039 0.248 9963 Planarity : 0.004 0.055 11210 Dihedral : 14.226 89.235 23721 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.13 % Favored : 92.66 % Rotamer: Outliers : 9.38 % Allowed : 10.18 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.08), residues: 7998 helix: -0.75 (0.06), residues: 5386 sheet: -1.72 (0.24), residues: 402 loop : -3.05 (0.12), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 507 HIS 0.006 0.001 HIS A1231 PHE 0.019 0.001 PHE X 294 TYR 0.018 0.001 TYR A 860 ARG 0.005 0.000 ARG A1076 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1485 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 630 poor density : 855 time to evaluate : 5.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.8272 (mmt) cc_final: 0.8006 (mmm) REVERT: A 412 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8636 (pp) REVERT: A 485 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8359 (tp) REVERT: A 638 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.8997 (mp) REVERT: A 779 MET cc_start: 0.8151 (mmt) cc_final: 0.7945 (mmt) REVERT: A 866 ILE cc_start: 0.9156 (tp) cc_final: 0.8146 (tp) REVERT: A 1086 MET cc_start: 0.8612 (mtp) cc_final: 0.8372 (ttm) REVERT: A 1108 THR cc_start: 0.9750 (OUTLIER) cc_final: 0.9330 (m) REVERT: A 1181 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9340 (mm) REVERT: A 1203 MET cc_start: 0.8926 (mmt) cc_final: 0.8693 (tpp) REVERT: A 1244 ASP cc_start: 0.8397 (p0) cc_final: 0.8009 (p0) REVERT: A 1523 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9149 (tt) REVERT: A 1550 MET cc_start: 0.8057 (tpp) cc_final: 0.7741 (tpp) REVERT: A 1705 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8187 (mp10) REVERT: A 1805 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.5829 (tpt) REVERT: A 1928 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9237 (mm) REVERT: B 8 TRP cc_start: 0.5186 (t60) cc_final: 0.4980 (t60) REVERT: B 14 TRP cc_start: 0.5866 (OUTLIER) cc_final: 0.4284 (p-90) REVERT: B 16 TRP cc_start: 0.1909 (OUTLIER) cc_final: 0.1190 (m100) REVERT: C 133 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8532 (mt-10) REVERT: C 237 ILE cc_start: 0.9589 (OUTLIER) cc_final: 0.9325 (tp) REVERT: C 373 HIS cc_start: 0.7424 (t-170) cc_final: 0.7127 (t-170) REVERT: C 551 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8702 (mtm-85) REVERT: D 27 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8011 (tm-30) REVERT: D 31 GLN cc_start: 0.9253 (tt0) cc_final: 0.9008 (tp40) REVERT: E 73 ASP cc_start: 0.8567 (m-30) cc_final: 0.8099 (m-30) REVERT: E 76 VAL cc_start: 0.9133 (m) cc_final: 0.8484 (p) REVERT: F 494 HIS cc_start: 0.9063 (OUTLIER) cc_final: 0.8578 (p-80) REVERT: F 513 SER cc_start: 0.8551 (m) cc_final: 0.8036 (p) REVERT: F 519 GLU cc_start: 0.8682 (pt0) cc_final: 0.8367 (pp20) REVERT: F 636 ASN cc_start: 0.9289 (OUTLIER) cc_final: 0.8937 (t0) REVERT: F 679 GLN cc_start: 0.8497 (mt0) cc_final: 0.7906 (pp30) REVERT: G 8 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8007 (ttm-80) REVERT: G 17 GLU cc_start: 0.8977 (tp30) cc_final: 0.8570 (tm-30) REVERT: G 21 ASN cc_start: 0.8342 (m-40) cc_final: 0.7766 (m-40) REVERT: H 30 ARG cc_start: 0.9384 (OUTLIER) cc_final: 0.9064 (mmp80) REVERT: H 71 CYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8691 (t) REVERT: H 463 MET cc_start: 0.9277 (tpp) cc_final: 0.8821 (tpp) REVERT: H 568 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: H 667 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7912 (pp30) REVERT: H 736 GLU cc_start: 0.7997 (tp30) cc_final: 0.7375 (tp30) REVERT: H 758 MET cc_start: 0.8415 (tpp) cc_final: 0.8105 (tpp) REVERT: I 267 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8895 (tt) REVERT: I 305 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8789 (mmm) REVERT: I 341 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8317 (t80) REVERT: I 411 MET cc_start: 0.9140 (ttp) cc_final: 0.8924 (ttm) REVERT: I 440 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7955 (mtm) REVERT: J 214 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8119 (ptmm) REVERT: J 239 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8032 (mt-10) REVERT: J 295 TYR cc_start: 0.8752 (m-80) cc_final: 0.8483 (m-10) REVERT: J 362 GLN cc_start: 0.9505 (OUTLIER) cc_final: 0.9293 (mt0) REVERT: J 407 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8732 (mp0) REVERT: J 437 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7710 (t0) REVERT: J 477 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8974 (mm110) REVERT: K 175 MET cc_start: 0.8400 (mtt) cc_final: 0.8110 (mtm) REVERT: K 193 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7369 (mt) REVERT: K 311 MET cc_start: 0.8728 (ttm) cc_final: 0.8380 (ttm) REVERT: K 347 GLU cc_start: 0.8705 (tp30) cc_final: 0.8411 (tp30) REVERT: L 66 ILE cc_start: 0.9719 (mt) cc_final: 0.9493 (mt) REVERT: L 71 LYS cc_start: 0.8840 (tttm) cc_final: 0.8233 (tptm) REVERT: L 100 ASN cc_start: 0.9480 (OUTLIER) cc_final: 0.9201 (m-40) REVERT: L 153 MET cc_start: 0.9196 (tpp) cc_final: 0.8881 (mmm) REVERT: L 163 GLU cc_start: 0.7820 (pt0) cc_final: 0.7608 (pt0) REVERT: M 8 ASP cc_start: 0.8108 (t0) cc_final: 0.7517 (t0) REVERT: M 10 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7671 (pmm150) REVERT: M 28 ASP cc_start: 0.8469 (m-30) cc_final: 0.8245 (m-30) REVERT: M 51 LYS cc_start: 0.8921 (ptpt) cc_final: 0.8698 (ttpp) REVERT: M 54 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8500 (mt-10) REVERT: M 55 MET cc_start: 0.9079 (tpt) cc_final: 0.8819 (tpp) REVERT: N 135 TRP cc_start: 0.8449 (OUTLIER) cc_final: 0.8053 (m-90) REVERT: N 387 LEU cc_start: 0.8977 (mt) cc_final: 0.8414 (mt) REVERT: N 417 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8461 (tp) REVERT: N 431 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6321 (tpm170) REVERT: N 533 PHE cc_start: 0.5359 (OUTLIER) cc_final: 0.4374 (m-80) REVERT: N 589 PHE cc_start: 0.3415 (OUTLIER) cc_final: 0.3040 (p90) REVERT: N 622 TYR cc_start: 0.4129 (OUTLIER) cc_final: 0.3030 (t80) REVERT: N 637 TRP cc_start: 0.7359 (m100) cc_final: 0.6278 (m100) REVERT: N 682 SER cc_start: 0.8792 (t) cc_final: 0.8048 (p) REVERT: N 693 ARG cc_start: 0.9148 (mtp85) cc_final: 0.8442 (tpm170) REVERT: N 713 PHE cc_start: 0.4866 (m-80) cc_final: 0.4227 (m-80) REVERT: N 775 ASN cc_start: 0.7892 (t0) cc_final: 0.7690 (t0) REVERT: O 57 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8863 (ttp80) REVERT: O 110 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8192 (pp30) REVERT: O 408 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9019 (mt) REVERT: O 508 MET cc_start: 0.8245 (mtt) cc_final: 0.8037 (mtm) REVERT: O 512 GLN cc_start: 0.9426 (OUTLIER) cc_final: 0.9037 (mp10) REVERT: P 182 LEU cc_start: 0.9724 (mp) cc_final: 0.9483 (mt) REVERT: P 229 MET cc_start: 0.9018 (mmm) cc_final: 0.8684 (mmm) REVERT: P 523 CYS cc_start: 0.7717 (t) cc_final: 0.7434 (p) REVERT: W 8 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.6911 (ttm-80) REVERT: X 88 PHE cc_start: 0.9324 (t80) cc_final: 0.9061 (t80) REVERT: X 156 ILE cc_start: 0.9573 (mt) cc_final: 0.9171 (mm) REVERT: X 178 LEU cc_start: 0.9498 (mt) cc_final: 0.9266 (mp) REVERT: X 196 LEU cc_start: 0.9560 (mt) cc_final: 0.9354 (mt) REVERT: X 303 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.7092 (p90) REVERT: X 304 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6602 (pp) REVERT: X 369 ASN cc_start: 0.8706 (m110) cc_final: 0.8127 (p0) REVERT: X 395 HIS cc_start: 0.8290 (m-70) cc_final: 0.7624 (m90) REVERT: X 401 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8369 (ttt-90) REVERT: X 432 ASN cc_start: 0.9413 (OUTLIER) cc_final: 0.9163 (m110) REVERT: X 435 LYS cc_start: 0.9331 (tptt) cc_final: 0.9102 (mtmt) REVERT: X 447 LEU cc_start: 0.9074 (mt) cc_final: 0.8812 (tp) REVERT: X 486 LEU cc_start: 0.5460 (OUTLIER) cc_final: 0.5182 (mt) REVERT: Y 52 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.7642 (m-40) REVERT: Y 95 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8199 (m110) REVERT: Y 288 LYS cc_start: 0.8738 (mttt) cc_final: 0.8303 (mmtm) REVERT: Y 293 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9083 (tppt) REVERT: Y 295 GLU cc_start: 0.8504 (mt-10) cc_final: 0.7742 (mp0) REVERT: Y 308 MET cc_start: 0.8888 (mmt) cc_final: 0.8278 (mmp) REVERT: Y 414 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8458 (mm) REVERT: Y 549 MET cc_start: 0.8786 (mmt) cc_final: 0.8332 (ppp) REVERT: Y 550 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8442 (pt0) REVERT: Y 551 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8146 (ptpt) outliers start: 630 outliers final: 212 residues processed: 1402 average time/residue: 0.6169 time to fit residues: 1449.9403 Evaluate side-chains 785 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 519 time to evaluate : 5.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1024 MET Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1036 ASP Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1417 ASP Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1437 ASN Chi-restraints excluded: chain A residue 1496 MET Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1546 THR Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1607 ARG Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1705 GLN Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1805 MET Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain A residue 1911 PHE Chi-restraints excluded: chain A residue 1920 GLN Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 536 CYS Chi-restraints excluded: chain C residue 551 ARG Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 487 ILE Chi-restraints excluded: chain F residue 494 HIS Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 636 ASN Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 733 VAL Chi-restraints excluded: chain G residue 8 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 530 ASN Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain H residue 667 GLN Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 305 MET Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 425 MET Chi-restraints excluded: chain I residue 440 MET Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 656 THR Chi-restraints excluded: chain I residue 663 ASP Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 362 GLN Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 407 GLU Chi-restraints excluded: chain J residue 437 ASN Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 214 LYS Chi-restraints excluded: chain K residue 225 ASP Chi-restraints excluded: chain K residue 234 VAL Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 352 GLN Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 376 LEU Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 438 GLU Chi-restraints excluded: chain K residue 475 ILE Chi-restraints excluded: chain K residue 503 HIS Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 100 ASN Chi-restraints excluded: chain L residue 144 ASN Chi-restraints excluded: chain L residue 154 ARG Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 16 ASP Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain N residue 135 TRP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 392 ASN Chi-restraints excluded: chain N residue 409 VAL Chi-restraints excluded: chain N residue 417 LEU Chi-restraints excluded: chain N residue 431 ARG Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 533 PHE Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 589 PHE Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 650 LEU Chi-restraints excluded: chain N residue 667 LEU Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 110 GLN Chi-restraints excluded: chain O residue 250 PHE Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 441 GLN Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 512 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 550 VAL Chi-restraints excluded: chain O residue 567 LEU Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 590 LEU Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 641 LEU Chi-restraints excluded: chain O residue 645 HIS Chi-restraints excluded: chain O residue 654 ASP Chi-restraints excluded: chain O residue 691 ILE Chi-restraints excluded: chain O residue 710 ILE Chi-restraints excluded: chain O residue 751 LEU Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 172 LEU Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 183 ASP Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 495 GLN Chi-restraints excluded: chain W residue 8 ARG Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 233 LEU Chi-restraints excluded: chain X residue 271 VAL Chi-restraints excluded: chain X residue 286 ASP Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain X residue 401 ARG Chi-restraints excluded: chain X residue 432 ASN Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 486 LEU Chi-restraints excluded: chain X residue 503 LEU Chi-restraints excluded: chain Y residue 52 ASN Chi-restraints excluded: chain Y residue 95 ASN Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 293 LYS Chi-restraints excluded: chain Y residue 354 ARG Chi-restraints excluded: chain Y residue 414 ILE Chi-restraints excluded: chain Y residue 423 ILE Chi-restraints excluded: chain Y residue 445 THR Chi-restraints excluded: chain Y residue 496 ILE Chi-restraints excluded: chain Y residue 530 ASP Chi-restraints excluded: chain Y residue 551 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 677 optimal weight: 10.0000 chunk 607 optimal weight: 5.9990 chunk 337 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 410 optimal weight: 9.9990 chunk 324 optimal weight: 20.0000 chunk 628 optimal weight: 0.9980 chunk 243 optimal weight: 10.0000 chunk 382 optimal weight: 20.0000 chunk 467 optimal weight: 9.9990 chunk 728 optimal weight: 6.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN A 125 GLN A 162 HIS ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 HIS ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN A 623 GLN A 636 GLN A 776 ASN ** A 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 GLN A1106 ASN A1124 ASN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 ASN A1231 HIS A1247 HIS A1359 ASN A1481 ASN A1511 ASN A1599 ASN ** A1602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1705 GLN A1795 GLN A1920 GLN B 31 ASN B 50 GLN B 53 HIS B 71 GLN C 71 GLN C 82 GLN C 197 HIS C 202 HIS C 249 GLN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS C 321 HIS C 361 ASN ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 ASN C 479 GLN C 488 GLN C 552 GLN D 31 GLN D 38 GLN F 486 ASN ** F 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 547 GLN F 595 GLN F 667 GLN F 702 ASN F 716 ASN H 14 GLN H 90 GLN H 145 ASN H 166 GLN H 455 GLN ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 497 ASN H 545 HIS H 580 GLN H 583 HIS H 595 GLN ** H 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 648 GLN ** H 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 323 ASN ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 GLN J 38 GLN J 80 HIS J 271 HIS J 342 HIS J 352 GLN J 362 GLN J 406 HIS J 477 GLN J 503 HIS K 18 GLN K 38 GLN ** K 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 HIS ** K 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 15 GLN L 101 ASN L 128 HIS L 138 GLN L 146 GLN L 155 GLN N 80 GLN N 97 GLN N 170 GLN N 174 GLN ** N 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 329 GLN N 541 ASN N 722 GLN N 759 GLN O 69 GLN O 88 GLN O 219 GLN O 276 HIS O 318 GLN O 342 HIS O 370 HIS ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 460 GLN O 472 HIS ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 565 GLN O 617 GLN O 680 GLN P 71 GLN P 163 GLN P 249 GLN P 268 GLN P 299 ASN P 305 ASN ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 361 ASN P 386 GLN P 390 HIS P 426 HIS P 427 GLN ** P 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 485 GLN P 488 GLN ** P 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 518 GLN X 40 HIS X 78 GLN X 184 GLN X 247 HIS X 251 ASN X 289 ASN X 298 GLN X 337 GLN X 371 ASN ** X 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 50 HIS Y 66 ASN ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 367 GLN Y 385 ASN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 543 GLN Total number of N/Q/H flips: 125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 65197 Z= 0.322 Angle : 0.695 17.742 88353 Z= 0.358 Chirality : 0.042 0.284 9963 Planarity : 0.004 0.058 11210 Dihedral : 9.115 85.332 9357 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.92 % Favored : 92.97 % Rotamer: Outliers : 6.42 % Allowed : 14.81 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.09), residues: 7998 helix: 0.47 (0.07), residues: 5436 sheet: -1.31 (0.25), residues: 398 loop : -2.83 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 637 HIS 0.011 0.001 HIS J 86 PHE 0.037 0.002 PHE P 221 TYR 0.021 0.001 TYR C 364 ARG 0.010 0.001 ARG Y 513 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 431 poor density : 549 time to evaluate : 5.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 SER cc_start: 0.7224 (p) cc_final: 0.6758 (p) REVERT: A 412 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8760 (pp) REVERT: A 638 LEU cc_start: 0.9749 (OUTLIER) cc_final: 0.9364 (mp) REVERT: A 945 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: A 1057 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7308 (mm) REVERT: A 1181 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9336 (mm) REVERT: A 1203 MET cc_start: 0.8896 (mmt) cc_final: 0.8692 (tpp) REVERT: A 1244 ASP cc_start: 0.8431 (p0) cc_final: 0.8105 (p0) REVERT: A 1271 GLU cc_start: 0.7942 (tt0) cc_final: 0.7408 (tt0) REVERT: A 1523 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9219 (tt) REVERT: B 14 TRP cc_start: 0.5939 (OUTLIER) cc_final: 0.4219 (p-90) REVERT: B 16 TRP cc_start: 0.3735 (OUTLIER) cc_final: 0.0627 (m100) REVERT: C 232 PHE cc_start: 0.9668 (OUTLIER) cc_final: 0.9121 (m-80) REVERT: C 373 HIS cc_start: 0.7520 (t-170) cc_final: 0.7025 (t-170) REVERT: C 389 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.9036 (mmt180) REVERT: C 551 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8672 (mtm-85) REVERT: D 27 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8023 (tm-30) REVERT: D 31 GLN cc_start: 0.9229 (tt0) cc_final: 0.9020 (tp40) REVERT: E 73 ASP cc_start: 0.8357 (m-30) cc_final: 0.8087 (m-30) REVERT: F 463 MET cc_start: 0.8189 (mmm) cc_final: 0.7964 (mmt) REVERT: F 494 HIS cc_start: 0.8836 (OUTLIER) cc_final: 0.8419 (p-80) REVERT: F 636 ASN cc_start: 0.9402 (OUTLIER) cc_final: 0.9116 (t0) REVERT: G 17 GLU cc_start: 0.8703 (tp30) cc_final: 0.8366 (tm-30) REVERT: G 21 ASN cc_start: 0.8290 (m-40) cc_final: 0.6069 (m-40) REVERT: H 30 ARG cc_start: 0.9423 (OUTLIER) cc_final: 0.8998 (mmp80) REVERT: H 104 ASP cc_start: 0.8966 (OUTLIER) cc_final: 0.8744 (p0) REVERT: H 568 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8386 (mp0) REVERT: H 643 MET cc_start: 0.8508 (tpp) cc_final: 0.8192 (ttt) REVERT: H 667 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8273 (pp30) REVERT: H 704 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9257 (tp) REVERT: I 267 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8911 (tt) REVERT: I 305 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8813 (mmm) REVERT: I 341 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8284 (t80) REVERT: I 647 GLU cc_start: 0.9506 (mt-10) cc_final: 0.9218 (tm-30) REVERT: J 214 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8117 (ptmm) REVERT: J 239 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8045 (mt-10) REVERT: J 362 GLN cc_start: 0.9492 (OUTLIER) cc_final: 0.9224 (mt0) REVERT: J 405 MET cc_start: 0.8968 (mtp) cc_final: 0.8728 (mtp) REVERT: J 407 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8691 (mp0) REVERT: J 437 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7688 (t0) REVERT: J 477 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8751 (mm110) REVERT: J 497 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.7999 (p0) REVERT: K 193 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7469 (mt) REVERT: K 311 MET cc_start: 0.8620 (ttm) cc_final: 0.8314 (ttm) REVERT: K 347 GLU cc_start: 0.8822 (tp30) cc_final: 0.8443 (tp30) REVERT: K 354 MET cc_start: 0.8794 (ttm) cc_final: 0.8374 (ttm) REVERT: K 364 MET cc_start: 0.9119 (mtp) cc_final: 0.8753 (mtp) REVERT: K 371 MET cc_start: 0.8864 (mtm) cc_final: 0.8559 (mtm) REVERT: K 378 TYR cc_start: 0.9173 (OUTLIER) cc_final: 0.8854 (m-10) REVERT: L 71 LYS cc_start: 0.8718 (tttm) cc_final: 0.8388 (tptm) REVERT: L 115 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7507 (tm-30) REVERT: L 153 MET cc_start: 0.9221 (tpp) cc_final: 0.8876 (mmm) REVERT: M 8 ASP cc_start: 0.8201 (t0) cc_final: 0.7536 (t0) REVERT: M 16 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8343 (p0) REVERT: M 51 LYS cc_start: 0.9033 (ptpt) cc_final: 0.8760 (tmtt) REVERT: M 52 GLU cc_start: 0.8916 (pt0) cc_final: 0.8608 (pp20) REVERT: M 54 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8513 (mt-10) REVERT: M 55 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8822 (tpp) REVERT: N 123 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7773 (m-30) REVERT: N 135 TRP cc_start: 0.8420 (OUTLIER) cc_final: 0.8000 (m-90) REVERT: N 516 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8772 (pt) REVERT: N 533 PHE cc_start: 0.5521 (OUTLIER) cc_final: 0.4404 (m-80) REVERT: N 622 TYR cc_start: 0.4442 (OUTLIER) cc_final: 0.3298 (t80) REVERT: O 57 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8714 (ttp80) REVERT: O 110 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8197 (pp30) REVERT: O 138 HIS cc_start: 0.9066 (OUTLIER) cc_final: 0.8235 (t-90) REVERT: O 408 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8984 (mt) REVERT: O 508 MET cc_start: 0.8325 (mtt) cc_final: 0.8070 (mtm) REVERT: O 510 CYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8043 (m) REVERT: O 512 GLN cc_start: 0.9434 (OUTLIER) cc_final: 0.9072 (mp10) REVERT: P 119 MET cc_start: 0.8936 (tpp) cc_final: 0.8627 (tpp) REVERT: P 183 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8843 (m-30) REVERT: P 523 CYS cc_start: 0.7491 (t) cc_final: 0.7220 (p) REVERT: W 8 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.6992 (ttm-80) REVERT: X 196 LEU cc_start: 0.9572 (mt) cc_final: 0.9362 (mt) REVERT: X 304 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6530 (pp) REVERT: X 369 ASN cc_start: 0.8678 (m110) cc_final: 0.8060 (p0) REVERT: X 383 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8713 (tm) REVERT: X 386 MET cc_start: 0.8452 (mmm) cc_final: 0.8139 (mmm) REVERT: X 395 HIS cc_start: 0.7944 (m-70) cc_final: 0.7597 (m90) REVERT: X 429 MET cc_start: 0.7975 (tpp) cc_final: 0.7662 (tpp) REVERT: X 435 LYS cc_start: 0.9356 (tptt) cc_final: 0.9115 (mtmt) REVERT: X 447 LEU cc_start: 0.9044 (mt) cc_final: 0.8772 (tp) REVERT: X 486 LEU cc_start: 0.5358 (OUTLIER) cc_final: 0.5084 (mt) REVERT: Y 52 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7628 (m-40) REVERT: Y 293 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.9111 (tppt) REVERT: Y 295 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7877 (mp0) REVERT: Y 299 MET cc_start: 0.9063 (mtt) cc_final: 0.8600 (mtp) REVERT: Y 308 MET cc_start: 0.8777 (mmt) cc_final: 0.8084 (mmp) REVERT: Y 322 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8853 (mp0) REVERT: Y 414 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8448 (mm) REVERT: Y 551 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8237 (ptpt) outliers start: 431 outliers final: 260 residues processed: 929 average time/residue: 0.5807 time to fit residues: 934.1484 Evaluate side-chains 771 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 460 time to evaluate : 6.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1024 MET Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1036 ASP Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1417 ASP Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1496 MET Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1507 THR Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1546 THR Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1607 ARG Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1641 THR Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1694 ASP Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1805 MET Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain A residue 1911 PHE Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 536 CYS Chi-restraints excluded: chain C residue 551 ARG Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 487 ILE Chi-restraints excluded: chain F residue 494 HIS Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 634 HIS Chi-restraints excluded: chain F residue 636 ASN Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 480 ASN Chi-restraints excluded: chain H residue 530 ASN Chi-restraints excluded: chain H residue 563 ASP Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain H residue 612 VAL Chi-restraints excluded: chain H residue 667 GLN Chi-restraints excluded: chain H residue 704 LEU Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 305 MET Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 505 SER Chi-restraints excluded: chain I residue 656 THR Chi-restraints excluded: chain I residue 663 ASP Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 362 GLN Chi-restraints excluded: chain J residue 385 LYS Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 407 GLU Chi-restraints excluded: chain J residue 418 TRP Chi-restraints excluded: chain J residue 437 ASN Chi-restraints excluded: chain J residue 442 ASP Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain J residue 497 ASN Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 214 LYS Chi-restraints excluded: chain K residue 234 VAL Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 352 GLN Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 438 GLU Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain K residue 442 ASP Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 144 ASN Chi-restraints excluded: chain L residue 154 ARG Chi-restraints excluded: chain M residue 16 ASP Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 135 TRP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 392 ASN Chi-restraints excluded: chain N residue 409 VAL Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 516 ILE Chi-restraints excluded: chain N residue 521 SER Chi-restraints excluded: chain N residue 533 PHE Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 650 LEU Chi-restraints excluded: chain N residue 678 LEU Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 691 LEU Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain N residue 773 ILE Chi-restraints excluded: chain N residue 817 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 110 GLN Chi-restraints excluded: chain O residue 138 HIS Chi-restraints excluded: chain O residue 250 PHE Chi-restraints excluded: chain O residue 264 VAL Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 369 VAL Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 441 GLN Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 510 CYS Chi-restraints excluded: chain O residue 512 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 550 VAL Chi-restraints excluded: chain O residue 567 LEU Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 641 LEU Chi-restraints excluded: chain O residue 645 HIS Chi-restraints excluded: chain O residue 654 ASP Chi-restraints excluded: chain O residue 667 VAL Chi-restraints excluded: chain O residue 691 ILE Chi-restraints excluded: chain O residue 710 ILE Chi-restraints excluded: chain O residue 751 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 183 ASP Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 435 MET Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 495 GLN Chi-restraints excluded: chain W residue 8 ARG Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain X residue 233 LEU Chi-restraints excluded: chain X residue 271 VAL Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 456 VAL Chi-restraints excluded: chain X residue 486 LEU Chi-restraints excluded: chain X residue 503 LEU Chi-restraints excluded: chain Y residue 52 ASN Chi-restraints excluded: chain Y residue 147 THR Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 172 ASN Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain Y residue 293 LYS Chi-restraints excluded: chain Y residue 354 ARG Chi-restraints excluded: chain Y residue 408 ASP Chi-restraints excluded: chain Y residue 414 ILE Chi-restraints excluded: chain Y residue 423 ILE Chi-restraints excluded: chain Y residue 445 THR Chi-restraints excluded: chain Y residue 530 ASP Chi-restraints excluded: chain Y residue 551 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 404 optimal weight: 7.9990 chunk 226 optimal weight: 8.9990 chunk 606 optimal weight: 4.9990 chunk 495 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 729 optimal weight: 7.9990 chunk 788 optimal weight: 10.0000 chunk 649 optimal weight: 0.9980 chunk 723 optimal weight: 9.9990 chunk 248 optimal weight: 0.2980 chunk 585 optimal weight: 7.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1351 GLN A1359 ASN ** A1602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 HIS ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 ASN F 494 HIS F 495 HIS F 609 HIS F 636 ASN H 166 GLN ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 517 GLN ** H 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 266 ASN I 323 ASN I 345 GLN ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 GLN J 342 HIS J 503 HIS ** K 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 489 HIS L 15 GLN L 103 HIS ** N 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 276 HIS ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 460 GLN ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 741 HIS ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Y 337 GLN Y 369 ASN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 65197 Z= 0.272 Angle : 0.660 20.325 88353 Z= 0.338 Chirality : 0.041 0.229 9963 Planarity : 0.004 0.052 11210 Dihedral : 8.592 85.724 9259 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.90 % Favored : 93.01 % Rotamer: Outliers : 6.33 % Allowed : 15.63 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.09), residues: 7998 helix: 0.91 (0.07), residues: 5443 sheet: -1.19 (0.26), residues: 385 loop : -2.68 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 8 HIS 0.007 0.001 HIS F 657 PHE 0.021 0.001 PHE Y 71 TYR 0.021 0.001 TYR K 140 ARG 0.010 0.000 ARG N 693 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 425 poor density : 499 time to evaluate : 5.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 SER cc_start: 0.7249 (p) cc_final: 0.6844 (p) REVERT: A 412 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8681 (pp) REVERT: A 485 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8436 (tp) REVERT: A 668 MET cc_start: 0.7952 (mmm) cc_final: 0.7703 (mmm) REVERT: A 804 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8576 (t0) REVERT: A 945 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8207 (mp0) REVERT: A 1057 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7339 (mm) REVERT: A 1181 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9326 (mm) REVERT: A 1244 ASP cc_start: 0.8437 (p0) cc_final: 0.8105 (p0) REVERT: A 1271 GLU cc_start: 0.7933 (tt0) cc_final: 0.7324 (tt0) REVERT: A 1523 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9200 (tt) REVERT: A 1525 MET cc_start: 0.8912 (ttm) cc_final: 0.8475 (ttp) REVERT: A 1805 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7672 (tpp) REVERT: A 1810 GLU cc_start: 0.8512 (mp0) cc_final: 0.8210 (pm20) REVERT: B 14 TRP cc_start: 0.5666 (OUTLIER) cc_final: 0.4232 (p-90) REVERT: B 16 TRP cc_start: 0.3767 (OUTLIER) cc_final: 0.1334 (m100) REVERT: C 122 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8659 (ttp-170) REVERT: C 232 PHE cc_start: 0.9664 (OUTLIER) cc_final: 0.9046 (m-80) REVERT: C 237 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9311 (tp) REVERT: C 373 HIS cc_start: 0.7683 (t-170) cc_final: 0.7211 (t-170) REVERT: C 376 MET cc_start: 0.8945 (ttp) cc_final: 0.8508 (ttm) REVERT: C 389 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.9122 (mmt180) REVERT: C 424 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8544 (mmm-85) REVERT: C 551 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8703 (mtm-85) REVERT: D 27 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8080 (tm-30) REVERT: E 73 ASP cc_start: 0.8283 (m-30) cc_final: 0.8032 (m-30) REVERT: G 21 ASN cc_start: 0.7724 (m-40) cc_final: 0.6812 (m-40) REVERT: H 30 ARG cc_start: 0.9420 (OUTLIER) cc_final: 0.9017 (mmp80) REVERT: H 71 CYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8783 (t) REVERT: H 104 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8726 (p0) REVERT: H 558 ASP cc_start: 0.8331 (t0) cc_final: 0.8082 (t0) REVERT: H 568 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: H 667 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8217 (pp30) REVERT: H 704 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9257 (tp) REVERT: H 758 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.8000 (tpt) REVERT: I 64 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8813 (p) REVERT: I 267 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8909 (tt) REVERT: I 341 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8381 (t80) REVERT: I 647 GLU cc_start: 0.9534 (mt-10) cc_final: 0.9251 (tm-30) REVERT: J 214 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8399 (ttpt) REVERT: J 239 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8053 (mt-10) REVERT: J 407 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8687 (mm-30) REVERT: J 437 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.7739 (t0) REVERT: J 477 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8923 (mm110) REVERT: J 497 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8164 (p0) REVERT: K 175 MET cc_start: 0.8014 (mtm) cc_final: 0.7629 (mtm) REVERT: K 193 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7400 (mt) REVERT: K 249 MET cc_start: 0.8888 (mmm) cc_final: 0.8271 (tmm) REVERT: K 311 MET cc_start: 0.8642 (ttm) cc_final: 0.8403 (ttm) REVERT: K 347 GLU cc_start: 0.8863 (tp30) cc_final: 0.8485 (tp30) REVERT: K 354 MET cc_start: 0.8840 (ttm) cc_final: 0.8285 (ttm) REVERT: K 378 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8640 (m-10) REVERT: L 71 LYS cc_start: 0.8753 (tttm) cc_final: 0.8461 (tptm) REVERT: L 153 MET cc_start: 0.9263 (tpp) cc_final: 0.8926 (mmm) REVERT: M 8 ASP cc_start: 0.8021 (t0) cc_final: 0.7656 (t70) REVERT: M 51 LYS cc_start: 0.9015 (ptpt) cc_final: 0.8669 (tmtt) REVERT: M 52 GLU cc_start: 0.8914 (pt0) cc_final: 0.8593 (pp20) REVERT: M 54 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8433 (mt-10) REVERT: M 55 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8817 (tpp) REVERT: N 135 TRP cc_start: 0.8405 (OUTLIER) cc_final: 0.7996 (m-90) REVERT: N 172 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8596 (mpp) REVERT: N 383 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8391 (mt-10) REVERT: N 387 LEU cc_start: 0.8892 (mt) cc_final: 0.8485 (mt) REVERT: N 431 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6430 (tpm170) REVERT: N 533 PHE cc_start: 0.5563 (OUTLIER) cc_final: 0.4386 (m-80) REVERT: N 622 TYR cc_start: 0.4112 (OUTLIER) cc_final: 0.2976 (t80) REVERT: O 57 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8700 (ttp80) REVERT: O 110 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8173 (pp30) REVERT: O 264 VAL cc_start: 0.9390 (OUTLIER) cc_final: 0.9183 (p) REVERT: O 408 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9054 (mt) REVERT: O 508 MET cc_start: 0.8369 (mtt) cc_final: 0.8103 (mtm) REVERT: O 512 GLN cc_start: 0.9423 (OUTLIER) cc_final: 0.9051 (mp10) REVERT: P 119 MET cc_start: 0.8957 (tpp) cc_final: 0.8609 (tpp) REVERT: P 173 TYR cc_start: 0.8751 (t80) cc_final: 0.8344 (t80) REVERT: P 523 CYS cc_start: 0.7371 (t) cc_final: 0.7105 (p) REVERT: W 8 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.6724 (ttm-80) REVERT: X 174 MET cc_start: 0.9091 (tpp) cc_final: 0.8649 (tpp) REVERT: X 304 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6425 (pp) REVERT: X 383 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8735 (tm) REVERT: X 386 MET cc_start: 0.8594 (mmm) cc_final: 0.8290 (mmm) REVERT: X 395 HIS cc_start: 0.8030 (m-70) cc_final: 0.7715 (m90) REVERT: X 427 MET cc_start: 0.6522 (tpt) cc_final: 0.6166 (tpt) REVERT: X 435 LYS cc_start: 0.9344 (tptt) cc_final: 0.9094 (mtmt) REVERT: X 447 LEU cc_start: 0.8899 (mt) cc_final: 0.8546 (tp) REVERT: X 486 LEU cc_start: 0.5346 (OUTLIER) cc_final: 0.5070 (mt) REVERT: Y 52 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7781 (m-40) REVERT: Y 100 TYR cc_start: 0.7431 (m-80) cc_final: 0.7184 (m-80) REVERT: Y 102 MET cc_start: 0.9166 (mmm) cc_final: 0.8924 (mmm) REVERT: Y 293 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.9067 (tppt) REVERT: Y 295 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7733 (mp0) REVERT: Y 299 MET cc_start: 0.9083 (mtt) cc_final: 0.8589 (mtp) REVERT: Y 304 LEU cc_start: 0.9104 (tp) cc_final: 0.8702 (tt) REVERT: Y 308 MET cc_start: 0.8815 (mmt) cc_final: 0.8207 (mmt) REVERT: Y 322 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8804 (pm20) REVERT: Y 330 ARG cc_start: 0.9383 (OUTLIER) cc_final: 0.8895 (ttp80) REVERT: Y 414 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8326 (mm) REVERT: Y 549 MET cc_start: 0.8369 (mmt) cc_final: 0.8114 (mmm) outliers start: 425 outliers final: 264 residues processed: 875 average time/residue: 0.6200 time to fit residues: 938.1705 Evaluate side-chains 763 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 446 time to evaluate : 5.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1024 MET Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1036 ASP Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1417 ASP Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1496 MET Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1507 THR Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1546 THR Chi-restraints excluded: chain A residue 1560 MET Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1641 THR Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1694 ASP Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1805 MET Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain A residue 1911 PHE Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 424 ARG Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 536 CYS Chi-restraints excluded: chain C residue 551 ARG Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 487 ILE Chi-restraints excluded: chain F residue 494 HIS Chi-restraints excluded: chain F residue 519 GLU Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 634 HIS Chi-restraints excluded: chain F residue 643 MET Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 480 ASN Chi-restraints excluded: chain H residue 530 ASN Chi-restraints excluded: chain H residue 563 ASP Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain H residue 612 VAL Chi-restraints excluded: chain H residue 667 GLN Chi-restraints excluded: chain H residue 704 LEU Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain H residue 758 MET Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 302 ASP Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 505 SER Chi-restraints excluded: chain I residue 656 THR Chi-restraints excluded: chain I residue 663 ASP Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 385 LYS Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 407 GLU Chi-restraints excluded: chain J residue 437 ASN Chi-restraints excluded: chain J residue 442 ASP Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain J residue 492 MET Chi-restraints excluded: chain J residue 497 ASN Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 214 LYS Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 438 GLU Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain K residue 442 ASP Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 144 ASN Chi-restraints excluded: chain L residue 154 ARG Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 135 TRP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 172 MET Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 378 LEU Chi-restraints excluded: chain N residue 383 GLU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 392 ASN Chi-restraints excluded: chain N residue 394 CYS Chi-restraints excluded: chain N residue 409 VAL Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 431 ARG Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 521 SER Chi-restraints excluded: chain N residue 533 PHE Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 549 PHE Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 660 THR Chi-restraints excluded: chain N residue 678 LEU Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 691 LEU Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain N residue 768 LEU Chi-restraints excluded: chain N residue 773 ILE Chi-restraints excluded: chain N residue 817 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 110 GLN Chi-restraints excluded: chain O residue 138 HIS Chi-restraints excluded: chain O residue 250 PHE Chi-restraints excluded: chain O residue 257 SER Chi-restraints excluded: chain O residue 264 VAL Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 357 SER Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 369 VAL Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 441 GLN Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 512 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 550 VAL Chi-restraints excluded: chain O residue 567 LEU Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 645 HIS Chi-restraints excluded: chain O residue 654 ASP Chi-restraints excluded: chain O residue 691 ILE Chi-restraints excluded: chain O residue 710 ILE Chi-restraints excluded: chain O residue 751 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 495 GLN Chi-restraints excluded: chain W residue 8 ARG Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain X residue 271 VAL Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 486 LEU Chi-restraints excluded: chain X residue 503 LEU Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 52 ASN Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 172 ASN Chi-restraints excluded: chain Y residue 188 SER Chi-restraints excluded: chain Y residue 293 LYS Chi-restraints excluded: chain Y residue 330 ARG Chi-restraints excluded: chain Y residue 337 GLN Chi-restraints excluded: chain Y residue 354 ARG Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 408 ASP Chi-restraints excluded: chain Y residue 414 ILE Chi-restraints excluded: chain Y residue 423 ILE Chi-restraints excluded: chain Y residue 445 THR Chi-restraints excluded: chain Y residue 496 ILE Chi-restraints excluded: chain Y residue 530 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 720 optimal weight: 6.9990 chunk 548 optimal weight: 8.9990 chunk 378 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 348 optimal weight: 6.9990 chunk 489 optimal weight: 8.9990 chunk 732 optimal weight: 6.9990 chunk 775 optimal weight: 10.0000 chunk 382 optimal weight: 20.0000 chunk 693 optimal weight: 9.9990 chunk 208 optimal weight: 0.5980 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1359 ASN A1380 ASN ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1716 GLN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 342 HIS J 503 HIS ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 HIS ** N 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 775 ASN ** N 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 407 GLN ** P 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 184 GLN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 65197 Z= 0.418 Angle : 0.723 18.655 88353 Z= 0.372 Chirality : 0.043 0.307 9963 Planarity : 0.004 0.056 11210 Dihedral : 8.448 77.060 9210 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.68 % Favored : 92.23 % Rotamer: Outliers : 6.88 % Allowed : 16.54 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.09), residues: 7998 helix: 0.96 (0.07), residues: 5447 sheet: -1.25 (0.25), residues: 390 loop : -2.65 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 8 HIS 0.019 0.001 HIS J 503 PHE 0.021 0.002 PHE N 713 TYR 0.021 0.002 TYR N 184 ARG 0.006 0.001 ARG Y 513 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 462 poor density : 444 time to evaluate : 5.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 SER cc_start: 0.7274 (p) cc_final: 0.6842 (p) REVERT: A 412 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8844 (pp) REVERT: A 945 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8451 (mp0) REVERT: A 1271 GLU cc_start: 0.8038 (tt0) cc_final: 0.7453 (tt0) REVERT: A 1550 MET cc_start: 0.8604 (tpp) cc_final: 0.8273 (tpp) REVERT: A 1884 MET cc_start: 0.8790 (mmm) cc_final: 0.8446 (mmm) REVERT: B 14 TRP cc_start: 0.5759 (OUTLIER) cc_final: 0.4296 (p-90) REVERT: B 16 TRP cc_start: 0.4008 (OUTLIER) cc_final: 0.1597 (m100) REVERT: C 79 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8828 (pm20) REVERT: C 232 PHE cc_start: 0.9686 (OUTLIER) cc_final: 0.9069 (m-80) REVERT: C 360 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9216 (tt) REVERT: C 373 HIS cc_start: 0.7741 (t-170) cc_final: 0.7341 (t-170) REVERT: C 376 MET cc_start: 0.9018 (ttp) cc_final: 0.8718 (ttm) REVERT: C 551 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8625 (mtm-85) REVERT: E 73 ASP cc_start: 0.8222 (m-30) cc_final: 0.8012 (m-30) REVERT: F 463 MET cc_start: 0.8274 (mmt) cc_final: 0.8040 (mmm) REVERT: F 519 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8105 (tm-30) REVERT: G 17 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8526 (tm-30) REVERT: G 21 ASN cc_start: 0.7350 (m-40) cc_final: 0.6990 (m-40) REVERT: H 30 ARG cc_start: 0.9431 (OUTLIER) cc_final: 0.9019 (mmp80) REVERT: H 71 CYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8774 (t) REVERT: H 667 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8276 (pp30) REVERT: H 704 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9346 (tp) REVERT: I 64 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8746 (p) REVERT: I 267 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8919 (tt) REVERT: I 305 MET cc_start: 0.8993 (mmm) cc_final: 0.8534 (mmm) REVERT: I 341 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8250 (t80) REVERT: J 239 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8071 (mt-10) REVERT: J 407 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8685 (mm-30) REVERT: J 437 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.7800 (t0) REVERT: J 477 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.8996 (mm110) REVERT: J 497 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8344 (p0) REVERT: K 175 MET cc_start: 0.8011 (mtm) cc_final: 0.7684 (mtm) REVERT: K 193 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7365 (mt) REVERT: K 249 MET cc_start: 0.9021 (mmm) cc_final: 0.8232 (tmm) REVERT: K 311 MET cc_start: 0.8663 (ttm) cc_final: 0.8418 (ttm) REVERT: K 329 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8588 (tt) REVERT: K 354 MET cc_start: 0.8862 (ttm) cc_final: 0.8182 (ttm) REVERT: K 378 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.8500 (m-10) REVERT: L 71 LYS cc_start: 0.8793 (tttm) cc_final: 0.8577 (tptm) REVERT: L 153 MET cc_start: 0.9308 (tpp) cc_final: 0.8977 (mmm) REVERT: M 51 LYS cc_start: 0.9008 (ptpt) cc_final: 0.8595 (tmtt) REVERT: M 52 GLU cc_start: 0.8951 (pt0) cc_final: 0.8634 (pp20) REVERT: M 54 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8458 (mt-10) REVERT: M 55 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8762 (tpp) REVERT: N 135 TRP cc_start: 0.8433 (OUTLIER) cc_final: 0.8023 (m-90) REVERT: N 172 MET cc_start: 0.8928 (mpp) cc_final: 0.8573 (mpp) REVERT: N 383 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: N 431 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6323 (tpm170) REVERT: N 533 PHE cc_start: 0.5512 (OUTLIER) cc_final: 0.4262 (m-80) REVERT: N 622 TYR cc_start: 0.4038 (OUTLIER) cc_final: 0.2990 (t80) REVERT: N 646 MET cc_start: 0.3363 (tmm) cc_final: 0.2753 (tmm) REVERT: O 100 MET cc_start: 0.9086 (tpp) cc_final: 0.8502 (tpt) REVERT: O 110 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8136 (pp30) REVERT: O 408 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9085 (mm) REVERT: O 462 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8282 (m-40) REVERT: O 508 MET cc_start: 0.8370 (mtt) cc_final: 0.8070 (mtm) REVERT: O 512 GLN cc_start: 0.9429 (OUTLIER) cc_final: 0.9042 (mp10) REVERT: P 119 MET cc_start: 0.9089 (tpp) cc_final: 0.8692 (tpp) REVERT: P 173 TYR cc_start: 0.8844 (t80) cc_final: 0.8554 (t80) REVERT: P 307 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9045 (mp) REVERT: P 523 CYS cc_start: 0.7211 (t) cc_final: 0.6965 (p) REVERT: W 8 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7185 (ttm-80) REVERT: W 23 ARG cc_start: 0.8446 (tmm-80) cc_final: 0.8181 (tmm-80) REVERT: X 174 MET cc_start: 0.9053 (tpp) cc_final: 0.8777 (tpp) REVERT: X 196 LEU cc_start: 0.9376 (mt) cc_final: 0.8966 (pp) REVERT: X 304 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6354 (pp) REVERT: X 383 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8728 (tm) REVERT: X 386 MET cc_start: 0.8622 (mmm) cc_final: 0.8307 (mmm) REVERT: X 395 HIS cc_start: 0.8046 (m-70) cc_final: 0.7687 (m170) REVERT: X 427 MET cc_start: 0.6547 (tpt) cc_final: 0.6189 (tpt) REVERT: X 435 LYS cc_start: 0.9336 (tptt) cc_final: 0.9080 (mtmt) REVERT: X 447 LEU cc_start: 0.8923 (mt) cc_final: 0.8613 (tp) REVERT: X 486 LEU cc_start: 0.5358 (OUTLIER) cc_final: 0.5099 (mt) REVERT: Y 100 TYR cc_start: 0.7785 (m-80) cc_final: 0.7485 (m-80) REVERT: Y 102 MET cc_start: 0.9166 (mmm) cc_final: 0.8928 (mmm) REVERT: Y 293 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9092 (tppt) REVERT: Y 295 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7684 (mp0) REVERT: Y 299 MET cc_start: 0.9087 (mtt) cc_final: 0.8583 (mtp) REVERT: Y 304 LEU cc_start: 0.9169 (tp) cc_final: 0.8742 (tt) REVERT: Y 308 MET cc_start: 0.8890 (mmt) cc_final: 0.8269 (mmt) REVERT: Y 322 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8828 (mp0) REVERT: Y 330 ARG cc_start: 0.9429 (OUTLIER) cc_final: 0.8808 (ttp80) REVERT: Y 386 MET cc_start: 0.8899 (mmm) cc_final: 0.8673 (mmm) REVERT: Y 429 MET cc_start: 0.9400 (mtp) cc_final: 0.9069 (ppp) REVERT: Y 549 MET cc_start: 0.8380 (mmt) cc_final: 0.8137 (mmm) outliers start: 462 outliers final: 310 residues processed: 854 average time/residue: 0.5836 time to fit residues: 866.4444 Evaluate side-chains 776 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 426 time to evaluate : 5.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1024 MET Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1036 ASP Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1417 ASP Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1479 SER Chi-restraints excluded: chain A residue 1496 MET Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1507 THR Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1546 THR Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1641 THR Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1694 ASP Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain A residue 1911 PHE Chi-restraints excluded: chain A residue 1920 GLN Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 536 CYS Chi-restraints excluded: chain C residue 551 ARG Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 487 ILE Chi-restraints excluded: chain F residue 494 HIS Chi-restraints excluded: chain F residue 519 GLU Chi-restraints excluded: chain F residue 523 SER Chi-restraints excluded: chain F residue 607 LEU Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 634 HIS Chi-restraints excluded: chain F residue 643 MET Chi-restraints excluded: chain F residue 673 CYS Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 480 ASN Chi-restraints excluded: chain H residue 530 ASN Chi-restraints excluded: chain H residue 563 ASP Chi-restraints excluded: chain H residue 612 VAL Chi-restraints excluded: chain H residue 667 GLN Chi-restraints excluded: chain H residue 704 LEU Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 350 SER Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 505 SER Chi-restraints excluded: chain I residue 559 ASP Chi-restraints excluded: chain I residue 656 THR Chi-restraints excluded: chain I residue 663 ASP Chi-restraints excluded: chain I residue 746 MET Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 385 LYS Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 407 GLU Chi-restraints excluded: chain J residue 437 ASN Chi-restraints excluded: chain J residue 439 VAL Chi-restraints excluded: chain J residue 442 ASP Chi-restraints excluded: chain J residue 454 VAL Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain J residue 497 ASN Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 234 VAL Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 329 LEU Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 438 GLU Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain K residue 442 ASP Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 144 ASN Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain L residue 154 ARG Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 135 TRP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 378 LEU Chi-restraints excluded: chain N residue 383 GLU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 392 ASN Chi-restraints excluded: chain N residue 394 CYS Chi-restraints excluded: chain N residue 409 VAL Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 417 LEU Chi-restraints excluded: chain N residue 431 ARG Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 533 PHE Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 549 PHE Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 649 GLU Chi-restraints excluded: chain N residue 650 LEU Chi-restraints excluded: chain N residue 660 THR Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain N residue 773 ILE Chi-restraints excluded: chain N residue 817 LEU Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 110 GLN Chi-restraints excluded: chain O residue 138 HIS Chi-restraints excluded: chain O residue 250 PHE Chi-restraints excluded: chain O residue 257 SER Chi-restraints excluded: chain O residue 264 VAL Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 296 TYR Chi-restraints excluded: chain O residue 357 SER Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 369 VAL Chi-restraints excluded: chain O residue 370 HIS Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 441 GLN Chi-restraints excluded: chain O residue 448 MET Chi-restraints excluded: chain O residue 462 ASN Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 512 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 550 VAL Chi-restraints excluded: chain O residue 567 LEU Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 590 LEU Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 645 HIS Chi-restraints excluded: chain O residue 654 ASP Chi-restraints excluded: chain O residue 691 ILE Chi-restraints excluded: chain O residue 710 ILE Chi-restraints excluded: chain O residue 751 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 495 GLN Chi-restraints excluded: chain W residue 8 ARG Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain X residue 233 LEU Chi-restraints excluded: chain X residue 271 VAL Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 486 LEU Chi-restraints excluded: chain X residue 503 LEU Chi-restraints excluded: chain X residue 522 VAL Chi-restraints excluded: chain X residue 529 MET Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 172 ASN Chi-restraints excluded: chain Y residue 188 SER Chi-restraints excluded: chain Y residue 293 LYS Chi-restraints excluded: chain Y residue 330 ARG Chi-restraints excluded: chain Y residue 354 ARG Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 408 ASP Chi-restraints excluded: chain Y residue 414 ILE Chi-restraints excluded: chain Y residue 423 ILE Chi-restraints excluded: chain Y residue 445 THR Chi-restraints excluded: chain Y residue 496 ILE Chi-restraints excluded: chain Y residue 530 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 645 optimal weight: 0.9980 chunk 440 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 577 optimal weight: 30.0000 chunk 319 optimal weight: 10.0000 chunk 661 optimal weight: 2.9990 chunk 535 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 395 optimal weight: 9.9990 chunk 695 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1359 ASN A1899 HIS C 252 GLN ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 ASN ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 609 HIS H 636 ASN ** H 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 323 ASN I 362 HIS ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 696 GLN J 88 GLN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 541 ASN N 775 ASN O 276 HIS ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 197 HIS ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 506 GLN ** Y 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 65197 Z= 0.187 Angle : 0.640 19.472 88353 Z= 0.322 Chirality : 0.040 0.222 9963 Planarity : 0.004 0.056 11210 Dihedral : 8.135 82.911 9187 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.10 % Favored : 93.84 % Rotamer: Outliers : 5.49 % Allowed : 17.84 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.36 % Twisted Proline : 0.34 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.10), residues: 7998 helix: 1.30 (0.07), residues: 5461 sheet: -0.97 (0.26), residues: 378 loop : -2.54 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 8 HIS 0.007 0.001 HIS I 102 PHE 0.020 0.001 PHE Y 71 TYR 0.025 0.001 TYR A 670 ARG 0.009 0.000 ARG N 695 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 369 poor density : 511 time to evaluate : 5.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 SER cc_start: 0.7111 (p) cc_final: 0.6585 (p) REVERT: A 485 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8412 (tp) REVERT: A 804 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8576 (t0) REVERT: A 945 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: A 1181 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9251 (mm) REVERT: A 1244 ASP cc_start: 0.8237 (p0) cc_final: 0.7966 (p0) REVERT: A 1279 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8057 (tpt90) REVERT: A 1325 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9204 (mm) REVERT: A 1550 MET cc_start: 0.8439 (tpp) cc_final: 0.8170 (tpp) REVERT: A 1805 MET cc_start: 0.7966 (tpp) cc_final: 0.7359 (tpp) REVERT: A 1810 GLU cc_start: 0.8313 (mp0) cc_final: 0.8058 (mp0) REVERT: A 1884 MET cc_start: 0.8810 (mmm) cc_final: 0.8457 (mmm) REVERT: B 14 TRP cc_start: 0.5600 (OUTLIER) cc_final: 0.4216 (p-90) REVERT: B 16 TRP cc_start: 0.3783 (OUTLIER) cc_final: 0.1622 (m100) REVERT: C 232 PHE cc_start: 0.9644 (OUTLIER) cc_final: 0.8987 (m-80) REVERT: C 237 ILE cc_start: 0.9541 (OUTLIER) cc_final: 0.9337 (tp) REVERT: C 373 HIS cc_start: 0.7669 (t-170) cc_final: 0.7292 (t-170) REVERT: D 27 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8051 (tp30) REVERT: E 73 ASP cc_start: 0.8291 (m-30) cc_final: 0.8013 (m-30) REVERT: F 75 LEU cc_start: 0.9729 (tp) cc_final: 0.9462 (tt) REVERT: F 463 MET cc_start: 0.8352 (mmt) cc_final: 0.8128 (mmm) REVERT: G 17 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8415 (tm-30) REVERT: G 21 ASN cc_start: 0.7273 (m-40) cc_final: 0.6839 (m-40) REVERT: H 30 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.9146 (mmp80) REVERT: H 71 CYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8728 (t) REVERT: H 104 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8617 (p0) REVERT: H 667 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8119 (pp30) REVERT: I 80 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8539 (mt) REVERT: I 250 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8509 (ptp-170) REVERT: I 267 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8931 (tt) REVERT: I 305 MET cc_start: 0.8942 (mmm) cc_final: 0.8682 (mmt) REVERT: I 341 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.8411 (t80) REVERT: I 647 GLU cc_start: 0.9548 (mt-10) cc_final: 0.9271 (tm-30) REVERT: J 214 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8386 (ptmt) REVERT: J 239 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8078 (mt-10) REVERT: J 354 MET cc_start: 0.8654 (mmt) cc_final: 0.8261 (mmm) REVERT: J 407 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8653 (mm-30) REVERT: J 437 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7777 (t0) REVERT: J 497 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8384 (p0) REVERT: K 175 MET cc_start: 0.7885 (mtm) cc_final: 0.7523 (mtm) REVERT: K 193 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7229 (mt) REVERT: K 329 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8592 (tt) REVERT: K 347 GLU cc_start: 0.8863 (tp30) cc_final: 0.8421 (tp30) REVERT: L 12 ASP cc_start: 0.9308 (OUTLIER) cc_final: 0.8712 (t0) REVERT: L 71 LYS cc_start: 0.8766 (tttm) cc_final: 0.8549 (tptm) REVERT: L 153 MET cc_start: 0.9274 (tpp) cc_final: 0.9073 (mmm) REVERT: M 51 LYS cc_start: 0.8995 (ptpt) cc_final: 0.8741 (tmtt) REVERT: M 52 GLU cc_start: 0.8936 (pt0) cc_final: 0.8659 (pp20) REVERT: M 53 GLN cc_start: 0.8266 (pt0) cc_final: 0.8059 (pt0) REVERT: M 54 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8563 (mt-10) REVERT: M 55 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8749 (tpp) REVERT: N 123 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8048 (m-30) REVERT: N 135 TRP cc_start: 0.8368 (OUTLIER) cc_final: 0.8010 (m-90) REVERT: N 172 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8640 (mpp) REVERT: N 387 LEU cc_start: 0.8786 (mt) cc_final: 0.8247 (mt) REVERT: N 431 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6719 (tpm170) REVERT: N 533 PHE cc_start: 0.5580 (OUTLIER) cc_final: 0.4358 (m-80) REVERT: N 622 TYR cc_start: 0.3964 (OUTLIER) cc_final: 0.2964 (t80) REVERT: O 57 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8647 (ttp80) REVERT: O 264 VAL cc_start: 0.9355 (OUTLIER) cc_final: 0.9142 (p) REVERT: O 408 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9011 (mt) REVERT: O 462 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8075 (m-40) REVERT: O 508 MET cc_start: 0.8268 (mtt) cc_final: 0.7926 (mtt) REVERT: O 512 GLN cc_start: 0.9334 (OUTLIER) cc_final: 0.8928 (mp10) REVERT: P 119 MET cc_start: 0.8955 (tpp) cc_final: 0.8563 (tpp) REVERT: P 173 TYR cc_start: 0.8674 (t80) cc_final: 0.8342 (t80) REVERT: P 523 CYS cc_start: 0.7253 (t) cc_final: 0.7008 (p) REVERT: W 8 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.6984 (ttm-80) REVERT: W 23 ARG cc_start: 0.8562 (tmm-80) cc_final: 0.8190 (tmm-80) REVERT: X 174 MET cc_start: 0.8976 (tpp) cc_final: 0.8705 (tpp) REVERT: X 196 LEU cc_start: 0.9419 (mt) cc_final: 0.9021 (pp) REVERT: X 251 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8445 (t0) REVERT: X 304 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6263 (pp) REVERT: X 308 MET cc_start: 0.7820 (tmm) cc_final: 0.7584 (tmm) REVERT: X 383 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8855 (tm) REVERT: X 386 MET cc_start: 0.8734 (mmm) cc_final: 0.8435 (mmm) REVERT: X 395 HIS cc_start: 0.8005 (m-70) cc_final: 0.7356 (m-70) REVERT: X 427 MET cc_start: 0.6268 (tpt) cc_final: 0.5905 (tpt) REVERT: X 435 LYS cc_start: 0.9334 (tptt) cc_final: 0.9084 (mtmt) REVERT: X 447 LEU cc_start: 0.8859 (mt) cc_final: 0.8496 (tp) REVERT: Y 100 TYR cc_start: 0.7815 (m-80) cc_final: 0.7550 (m-80) REVERT: Y 102 MET cc_start: 0.9145 (mmm) cc_final: 0.8916 (mmm) REVERT: Y 293 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.9020 (tppt) REVERT: Y 295 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7603 (mp0) REVERT: Y 308 MET cc_start: 0.8860 (mmt) cc_final: 0.8239 (mmp) REVERT: Y 322 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8794 (mp0) REVERT: Y 330 ARG cc_start: 0.9378 (OUTLIER) cc_final: 0.8820 (ttp80) REVERT: Y 386 MET cc_start: 0.8936 (mmm) cc_final: 0.8717 (mmm) REVERT: Y 414 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8318 (mm) outliers start: 369 outliers final: 242 residues processed: 832 average time/residue: 0.5848 time to fit residues: 843.1938 Evaluate side-chains 741 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 455 time to evaluate : 5.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1024 MET Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1036 ASP Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1417 ASP Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1496 MET Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1546 THR Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1694 ASP Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 536 CYS Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 487 ILE Chi-restraints excluded: chain F residue 494 HIS Chi-restraints excluded: chain F residue 607 LEU Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 634 HIS Chi-restraints excluded: chain F residue 673 CYS Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 480 ASN Chi-restraints excluded: chain H residue 530 ASN Chi-restraints excluded: chain H residue 563 ASP Chi-restraints excluded: chain H residue 667 GLN Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 250 ARG Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 302 ASP Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 328 LYS Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 350 SER Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 656 THR Chi-restraints excluded: chain I residue 696 GLN Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 407 GLU Chi-restraints excluded: chain J residue 437 ASN Chi-restraints excluded: chain J residue 439 VAL Chi-restraints excluded: chain J residue 497 ASN Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 329 LEU Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 438 GLU Chi-restraints excluded: chain K residue 442 ASP Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 144 ASN Chi-restraints excluded: chain L residue 154 ARG Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 135 TRP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 172 MET Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 371 ARG Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 378 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 392 ASN Chi-restraints excluded: chain N residue 409 VAL Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 431 ARG Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 533 PHE Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 541 ASN Chi-restraints excluded: chain N residue 549 PHE Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 650 LEU Chi-restraints excluded: chain N residue 660 THR Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain N residue 768 LEU Chi-restraints excluded: chain N residue 773 ILE Chi-restraints excluded: chain N residue 814 VAL Chi-restraints excluded: chain N residue 817 LEU Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 138 HIS Chi-restraints excluded: chain O residue 250 PHE Chi-restraints excluded: chain O residue 257 SER Chi-restraints excluded: chain O residue 264 VAL Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 370 HIS Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 441 GLN Chi-restraints excluded: chain O residue 462 ASN Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 512 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 550 VAL Chi-restraints excluded: chain O residue 567 LEU Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 641 LEU Chi-restraints excluded: chain O residue 645 HIS Chi-restraints excluded: chain O residue 648 ILE Chi-restraints excluded: chain O residue 654 ASP Chi-restraints excluded: chain O residue 667 VAL Chi-restraints excluded: chain O residue 691 ILE Chi-restraints excluded: chain O residue 710 ILE Chi-restraints excluded: chain O residue 751 LEU Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 495 GLN Chi-restraints excluded: chain W residue 8 ARG Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 522 VAL Chi-restraints excluded: chain X residue 529 MET Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 188 SER Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 293 LYS Chi-restraints excluded: chain Y residue 330 ARG Chi-restraints excluded: chain Y residue 354 ARG Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 408 ASP Chi-restraints excluded: chain Y residue 414 ILE Chi-restraints excluded: chain Y residue 423 ILE Chi-restraints excluded: chain Y residue 445 THR Chi-restraints excluded: chain Y residue 530 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 260 optimal weight: 6.9990 chunk 698 optimal weight: 30.0000 chunk 153 optimal weight: 10.0000 chunk 455 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 775 optimal weight: 20.0000 chunk 644 optimal weight: 5.9990 chunk 359 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 256 optimal weight: 7.9990 chunk 407 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1359 ASN A1595 HIS ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 674 HIS H 754 HIS ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 477 GLN K 174 HIS ** K 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 541 ASN ** N 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 460 GLN ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 369 ASN ** Y 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 65197 Z= 0.225 Angle : 0.644 18.237 88353 Z= 0.324 Chirality : 0.040 0.248 9963 Planarity : 0.004 0.055 11210 Dihedral : 7.717 66.341 9132 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.78 % Favored : 93.16 % Rotamer: Outliers : 5.42 % Allowed : 18.70 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.10), residues: 7998 helix: 1.40 (0.07), residues: 5460 sheet: -0.89 (0.25), residues: 385 loop : -2.50 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 507 HIS 0.008 0.001 HIS I 102 PHE 0.021 0.001 PHE N 713 TYR 0.021 0.001 TYR N 184 ARG 0.007 0.000 ARG H 527 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 364 poor density : 472 time to evaluate : 5.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8353 (ptt-90) REVERT: A 372 SER cc_start: 0.7208 (p) cc_final: 0.6673 (p) REVERT: A 485 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8448 (tp) REVERT: A 804 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8576 (t0) REVERT: A 945 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: A 1110 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8382 (mmp80) REVERT: A 1181 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9321 (mm) REVERT: A 1325 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9238 (mm) REVERT: A 1527 MET cc_start: 0.7854 (mtm) cc_final: 0.7641 (mtm) REVERT: A 1550 MET cc_start: 0.8424 (tpp) cc_final: 0.7746 (tpp) REVERT: A 1793 MET cc_start: 0.8593 (mtm) cc_final: 0.8387 (mtm) REVERT: A 1805 MET cc_start: 0.7845 (tpp) cc_final: 0.7250 (tpp) REVERT: A 1810 GLU cc_start: 0.8334 (mp0) cc_final: 0.8113 (mp0) REVERT: A 1884 MET cc_start: 0.8826 (mmm) cc_final: 0.8362 (mmm) REVERT: A 1911 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7506 (p90) REVERT: B 14 TRP cc_start: 0.5643 (OUTLIER) cc_final: 0.4313 (p-90) REVERT: B 16 TRP cc_start: 0.3930 (OUTLIER) cc_final: 0.1764 (m100) REVERT: C 232 PHE cc_start: 0.9648 (OUTLIER) cc_final: 0.8995 (m-80) REVERT: C 237 ILE cc_start: 0.9553 (OUTLIER) cc_final: 0.9336 (tp) REVERT: C 373 HIS cc_start: 0.7692 (t-170) cc_final: 0.7393 (t-170) REVERT: D 42 GLN cc_start: 0.8377 (tm-30) cc_final: 0.8122 (tm-30) REVERT: D 47 LYS cc_start: 0.8748 (tppt) cc_final: 0.8537 (ttmt) REVERT: E 73 ASP cc_start: 0.8330 (m-30) cc_final: 0.8061 (m-30) REVERT: G 17 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8543 (tm-30) REVERT: G 21 ASN cc_start: 0.7304 (m-40) cc_final: 0.6939 (m-40) REVERT: H 30 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.8915 (mmp80) REVERT: H 71 CYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8731 (t) REVERT: H 667 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8129 (pp30) REVERT: H 729 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9014 (tt) REVERT: I 64 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8831 (p) REVERT: I 250 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8602 (ptp-170) REVERT: I 305 MET cc_start: 0.8943 (mmm) cc_final: 0.8676 (mmt) REVERT: I 341 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8392 (t80) REVERT: I 647 GLU cc_start: 0.9555 (mt-10) cc_final: 0.9265 (tm-30) REVERT: I 705 MET cc_start: 0.8524 (mtp) cc_final: 0.7760 (mmm) REVERT: I 717 MET cc_start: 0.6925 (tpt) cc_final: 0.6350 (tpt) REVERT: J 214 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8412 (ttpt) REVERT: J 239 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8080 (mt-10) REVERT: J 354 MET cc_start: 0.8697 (mmt) cc_final: 0.8325 (mmm) REVERT: J 407 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8679 (mm-30) REVERT: J 437 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.7790 (t0) REVERT: J 497 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8413 (p0) REVERT: K 175 MET cc_start: 0.7872 (mtm) cc_final: 0.7528 (mtm) REVERT: K 193 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7149 (mt) REVERT: K 329 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8569 (tt) REVERT: K 351 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7106 (p0) REVERT: K 354 MET cc_start: 0.8871 (ttm) cc_final: 0.7980 (ttt) REVERT: K 378 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8238 (m-10) REVERT: L 53 TYR cc_start: 0.8830 (p90) cc_final: 0.8606 (p90) REVERT: L 154 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7309 (mmp-170) REVERT: M 51 LYS cc_start: 0.8996 (ptpt) cc_final: 0.8737 (tmtt) REVERT: M 52 GLU cc_start: 0.8928 (pt0) cc_final: 0.8650 (pp20) REVERT: M 53 GLN cc_start: 0.8320 (pt0) cc_final: 0.8112 (pt0) REVERT: M 54 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8537 (mt-10) REVERT: M 55 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8737 (tpp) REVERT: N 123 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.7980 (m-30) REVERT: N 135 TRP cc_start: 0.8354 (OUTLIER) cc_final: 0.7983 (m-90) REVERT: N 172 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8651 (mpp) REVERT: N 387 LEU cc_start: 0.8828 (mt) cc_final: 0.8275 (mt) REVERT: N 431 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6438 (tpm170) REVERT: N 622 TYR cc_start: 0.4155 (OUTLIER) cc_final: 0.3195 (t80) REVERT: N 646 MET cc_start: 0.2923 (tmm) cc_final: 0.2448 (tmm) REVERT: O 57 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8709 (ttp80) REVERT: O 264 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9177 (p) REVERT: O 462 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8025 (m-40) REVERT: O 508 MET cc_start: 0.8317 (mtt) cc_final: 0.8027 (mtm) REVERT: O 512 GLN cc_start: 0.9329 (OUTLIER) cc_final: 0.8906 (mp10) REVERT: P 119 MET cc_start: 0.9020 (tpp) cc_final: 0.8737 (tpp) REVERT: P 173 TYR cc_start: 0.8741 (t80) cc_final: 0.8431 (t80) REVERT: P 307 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9000 (mp) REVERT: P 523 CYS cc_start: 0.7247 (t) cc_final: 0.7013 (p) REVERT: W 8 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.6950 (ttm-80) REVERT: W 23 ARG cc_start: 0.8556 (tmm-80) cc_final: 0.8144 (tmm-80) REVERT: X 148 MET cc_start: 0.9024 (mpp) cc_final: 0.8790 (mpp) REVERT: X 174 MET cc_start: 0.9022 (tpp) cc_final: 0.8771 (tpp) REVERT: X 304 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6167 (pp) REVERT: X 383 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8779 (tt) REVERT: X 386 MET cc_start: 0.8758 (mmm) cc_final: 0.8496 (mmm) REVERT: X 395 HIS cc_start: 0.8031 (m-70) cc_final: 0.7685 (m170) REVERT: X 427 MET cc_start: 0.6317 (tpt) cc_final: 0.5951 (tpt) REVERT: X 435 LYS cc_start: 0.9339 (tptt) cc_final: 0.9087 (mtmt) REVERT: X 447 LEU cc_start: 0.8857 (mt) cc_final: 0.8498 (tp) REVERT: Y 100 TYR cc_start: 0.8001 (m-80) cc_final: 0.7638 (m-80) REVERT: Y 293 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.9023 (tppt) REVERT: Y 295 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7630 (mp0) REVERT: Y 299 MET cc_start: 0.9055 (mtt) cc_final: 0.8631 (mtp) REVERT: Y 308 MET cc_start: 0.8884 (mmt) cc_final: 0.8251 (mmp) REVERT: Y 322 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8799 (mp0) REVERT: Y 330 ARG cc_start: 0.9402 (OUTLIER) cc_final: 0.8847 (ttp80) REVERT: Y 386 MET cc_start: 0.9024 (mmm) cc_final: 0.8808 (mmm) REVERT: Y 414 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8327 (mm) outliers start: 364 outliers final: 259 residues processed: 791 average time/residue: 0.5961 time to fit residues: 819.6782 Evaluate side-chains 753 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 449 time to evaluate : 6.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1024 MET Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1036 ASP Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1110 ARG Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1417 ASP Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1496 MET Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1507 THR Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1546 THR Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1641 THR Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1694 ASP Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain A residue 1911 PHE Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 536 CYS Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 481 CYS Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 487 ILE Chi-restraints excluded: chain F residue 494 HIS Chi-restraints excluded: chain F residue 607 LEU Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 634 HIS Chi-restraints excluded: chain F residue 673 CYS Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 480 ASN Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 530 ASN Chi-restraints excluded: chain H residue 563 ASP Chi-restraints excluded: chain H residue 667 GLN Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 250 ARG Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 284 ASP Chi-restraints excluded: chain I residue 302 ASP Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 328 LYS Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 350 SER Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 656 THR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 385 LYS Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 407 GLU Chi-restraints excluded: chain J residue 437 ASN Chi-restraints excluded: chain J residue 439 VAL Chi-restraints excluded: chain J residue 497 ASN Chi-restraints excluded: chain J residue 506 LEU Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 311 MET Chi-restraints excluded: chain K residue 329 LEU Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 438 GLU Chi-restraints excluded: chain K residue 442 ASP Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 144 ASN Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain L residue 154 ARG Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 135 TRP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 172 MET Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 371 ARG Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 378 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 392 ASN Chi-restraints excluded: chain N residue 409 VAL Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 431 ARG Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 500 ASP Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 541 ASN Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 624 LYS Chi-restraints excluded: chain N residue 650 LEU Chi-restraints excluded: chain N residue 678 LEU Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain N residue 768 LEU Chi-restraints excluded: chain N residue 773 ILE Chi-restraints excluded: chain N residue 814 VAL Chi-restraints excluded: chain N residue 817 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 138 HIS Chi-restraints excluded: chain O residue 250 PHE Chi-restraints excluded: chain O residue 257 SER Chi-restraints excluded: chain O residue 264 VAL Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 357 SER Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 370 HIS Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 441 GLN Chi-restraints excluded: chain O residue 462 ASN Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 512 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 550 VAL Chi-restraints excluded: chain O residue 567 LEU Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 641 LEU Chi-restraints excluded: chain O residue 645 HIS Chi-restraints excluded: chain O residue 648 ILE Chi-restraints excluded: chain O residue 654 ASP Chi-restraints excluded: chain O residue 710 ILE Chi-restraints excluded: chain O residue 751 LEU Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 495 GLN Chi-restraints excluded: chain W residue 8 ARG Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 522 VAL Chi-restraints excluded: chain X residue 529 MET Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 188 SER Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 293 LYS Chi-restraints excluded: chain Y residue 330 ARG Chi-restraints excluded: chain Y residue 354 ARG Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 408 ASP Chi-restraints excluded: chain Y residue 414 ILE Chi-restraints excluded: chain Y residue 445 THR Chi-restraints excluded: chain Y residue 530 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 748 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 442 optimal weight: 1.9990 chunk 566 optimal weight: 3.9990 chunk 439 optimal weight: 4.9990 chunk 653 optimal weight: 0.8980 chunk 433 optimal weight: 5.9990 chunk 772 optimal weight: 0.9980 chunk 483 optimal weight: 5.9990 chunk 471 optimal weight: 5.9990 chunk 356 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1359 ASN ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 ASN ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 497 ASN ** H 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 413 ASN I 523 HIS ** I 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 GLN ** J 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 241 HIS K 350 HIS L 104 ASN N 541 ASN ** N 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 ASN ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 531 GLN ** Y 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 65197 Z= 0.233 Angle : 0.650 18.800 88353 Z= 0.327 Chirality : 0.040 0.303 9963 Planarity : 0.004 0.055 11210 Dihedral : 7.578 65.019 9116 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.65 % Favored : 93.28 % Rotamer: Outliers : 5.34 % Allowed : 19.16 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.10), residues: 7998 helix: 1.48 (0.07), residues: 5455 sheet: -0.94 (0.25), residues: 392 loop : -2.44 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 752 HIS 0.010 0.001 HIS I 102 PHE 0.030 0.001 PHE I 514 TYR 0.023 0.001 TYR N 184 ARG 0.007 0.000 ARG H 527 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 359 poor density : 465 time to evaluate : 5.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 SER cc_start: 0.7225 (p) cc_final: 0.6671 (p) REVERT: A 485 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8474 (tp) REVERT: A 804 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8576 (t0) REVERT: A 945 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8127 (mp0) REVERT: A 1110 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8401 (mmp80) REVERT: A 1181 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9341 (mm) REVERT: A 1325 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9247 (mm) REVERT: A 1550 MET cc_start: 0.8361 (tpp) cc_final: 0.7639 (tpp) REVERT: A 1805 MET cc_start: 0.7848 (tpp) cc_final: 0.7165 (tpp) REVERT: A 1810 GLU cc_start: 0.8313 (mp0) cc_final: 0.8079 (mp0) REVERT: A 1911 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7225 (p90) REVERT: B 14 TRP cc_start: 0.5648 (OUTLIER) cc_final: 0.4329 (p-90) REVERT: B 16 TRP cc_start: 0.3884 (OUTLIER) cc_final: 0.1794 (m100) REVERT: C 232 PHE cc_start: 0.9651 (OUTLIER) cc_final: 0.9040 (m-80) REVERT: C 373 HIS cc_start: 0.7716 (t-170) cc_final: 0.7427 (t-170) REVERT: C 490 TYR cc_start: 0.9383 (OUTLIER) cc_final: 0.9148 (m-10) REVERT: D 47 LYS cc_start: 0.8791 (tppt) cc_final: 0.8578 (ttmt) REVERT: E 73 ASP cc_start: 0.8305 (m-30) cc_final: 0.8063 (m-30) REVERT: H 30 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.8886 (mmp80) REVERT: H 71 CYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8752 (t) REVERT: H 611 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8278 (m-10) REVERT: H 667 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8126 (pp30) REVERT: H 729 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9031 (tt) REVERT: I 64 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8771 (p) REVERT: I 250 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8566 (ptp-170) REVERT: I 305 MET cc_start: 0.8930 (mmm) cc_final: 0.8686 (mmt) REVERT: I 310 TRP cc_start: 0.8835 (OUTLIER) cc_final: 0.8365 (m100) REVERT: I 341 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.8420 (t80) REVERT: I 647 GLU cc_start: 0.9556 (mt-10) cc_final: 0.9265 (tm-30) REVERT: J 239 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8056 (mt-10) REVERT: J 354 MET cc_start: 0.8702 (mmt) cc_final: 0.8314 (mmm) REVERT: J 407 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8684 (mm-30) REVERT: J 437 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.7875 (t0) REVERT: K 175 MET cc_start: 0.7856 (mtm) cc_final: 0.7503 (mtm) REVERT: K 193 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7125 (mt) REVERT: K 329 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8568 (tt) REVERT: K 351 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7048 (p0) REVERT: K 354 MET cc_start: 0.8871 (ttm) cc_final: 0.8009 (ttt) REVERT: K 371 MET cc_start: 0.8856 (mtp) cc_final: 0.8531 (ttp) REVERT: K 378 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: L 12 ASP cc_start: 0.9211 (OUTLIER) cc_final: 0.8550 (t0) REVERT: L 53 TYR cc_start: 0.8951 (p90) cc_final: 0.8736 (p90) REVERT: L 154 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7006 (mmp-170) REVERT: M 51 LYS cc_start: 0.8993 (ptpt) cc_final: 0.8758 (tmtt) REVERT: M 52 GLU cc_start: 0.8932 (pt0) cc_final: 0.8590 (pp20) REVERT: M 54 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8505 (mt-10) REVERT: M 55 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8763 (tpp) REVERT: N 123 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: N 135 TRP cc_start: 0.8334 (OUTLIER) cc_final: 0.7990 (m-90) REVERT: N 172 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8653 (mpp) REVERT: N 383 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8458 (mp0) REVERT: N 387 LEU cc_start: 0.8823 (mt) cc_final: 0.8300 (mt) REVERT: N 431 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6479 (tpm170) REVERT: N 533 PHE cc_start: 0.5535 (OUTLIER) cc_final: 0.4300 (m-80) REVERT: N 622 TYR cc_start: 0.4161 (OUTLIER) cc_final: 0.3197 (t80) REVERT: N 646 MET cc_start: 0.2634 (tmm) cc_final: 0.2043 (tmm) REVERT: N 649 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7239 (pt0) REVERT: O 57 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8676 (ttp80) REVERT: O 60 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8960 (pt) REVERT: O 264 VAL cc_start: 0.9384 (OUTLIER) cc_final: 0.9170 (p) REVERT: O 408 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9068 (mt) REVERT: O 462 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8023 (m-40) REVERT: O 508 MET cc_start: 0.8315 (mtt) cc_final: 0.8039 (mtm) REVERT: O 512 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.8881 (mp10) REVERT: P 119 MET cc_start: 0.9028 (tpp) cc_final: 0.8742 (tpp) REVERT: P 173 TYR cc_start: 0.8754 (t80) cc_final: 0.8449 (t80) REVERT: P 307 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9021 (mp) REVERT: P 523 CYS cc_start: 0.7037 (t) cc_final: 0.6808 (p) REVERT: W 14 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.6691 (t0) REVERT: X 174 MET cc_start: 0.9033 (tpp) cc_final: 0.8782 (tpp) REVERT: X 304 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6119 (pp) REVERT: X 383 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8816 (tt) REVERT: X 386 MET cc_start: 0.8791 (mmm) cc_final: 0.8522 (mmm) REVERT: X 395 HIS cc_start: 0.8113 (m-70) cc_final: 0.7731 (m170) REVERT: X 427 MET cc_start: 0.6352 (tpt) cc_final: 0.5980 (tpt) REVERT: X 435 LYS cc_start: 0.9340 (tptt) cc_final: 0.9084 (mtmt) REVERT: X 447 LEU cc_start: 0.8891 (mt) cc_final: 0.8492 (tp) REVERT: Y 293 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.9005 (tppt) REVERT: Y 295 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7667 (mp0) REVERT: Y 299 MET cc_start: 0.9069 (mtt) cc_final: 0.8621 (mtp) REVERT: Y 322 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8801 (mp0) REVERT: Y 330 ARG cc_start: 0.9398 (OUTLIER) cc_final: 0.8825 (ttp80) REVERT: Y 386 MET cc_start: 0.9045 (mmm) cc_final: 0.8821 (mmm) REVERT: Y 414 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8325 (mm) outliers start: 359 outliers final: 262 residues processed: 779 average time/residue: 0.5691 time to fit residues: 770.8602 Evaluate side-chains 752 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 440 time to evaluate : 5.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1024 MET Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1036 ASP Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1110 ARG Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1417 ASP Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1496 MET Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1507 THR Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1546 THR Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1641 THR Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1694 ASP Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain A residue 1911 PHE Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 490 TYR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 536 CYS Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 481 CYS Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 487 ILE Chi-restraints excluded: chain F residue 494 HIS Chi-restraints excluded: chain F residue 607 LEU Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 634 HIS Chi-restraints excluded: chain F residue 643 MET Chi-restraints excluded: chain F residue 673 CYS Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 480 ASN Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 530 ASN Chi-restraints excluded: chain H residue 563 ASP Chi-restraints excluded: chain H residue 611 PHE Chi-restraints excluded: chain H residue 667 GLN Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 250 ARG Chi-restraints excluded: chain I residue 273 CYS Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 284 ASP Chi-restraints excluded: chain I residue 310 TRP Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 328 LYS Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 350 SER Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 656 THR Chi-restraints excluded: chain I residue 663 ASP Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 385 LYS Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 407 GLU Chi-restraints excluded: chain J residue 437 ASN Chi-restraints excluded: chain J residue 439 VAL Chi-restraints excluded: chain J residue 506 LEU Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 311 MET Chi-restraints excluded: chain K residue 329 LEU Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 438 GLU Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 144 ASN Chi-restraints excluded: chain L residue 154 ARG Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 135 TRP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 172 MET Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 371 ARG Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 378 LEU Chi-restraints excluded: chain N residue 383 GLU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 392 ASN Chi-restraints excluded: chain N residue 409 VAL Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 431 ARG Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 500 ASP Chi-restraints excluded: chain N residue 533 PHE Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 624 LYS Chi-restraints excluded: chain N residue 649 GLU Chi-restraints excluded: chain N residue 650 LEU Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain N residue 768 LEU Chi-restraints excluded: chain N residue 773 ILE Chi-restraints excluded: chain N residue 814 VAL Chi-restraints excluded: chain N residue 817 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 138 HIS Chi-restraints excluded: chain O residue 250 PHE Chi-restraints excluded: chain O residue 257 SER Chi-restraints excluded: chain O residue 264 VAL Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 296 TYR Chi-restraints excluded: chain O residue 357 SER Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 370 HIS Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 441 GLN Chi-restraints excluded: chain O residue 462 ASN Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 512 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 550 VAL Chi-restraints excluded: chain O residue 567 LEU Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 641 LEU Chi-restraints excluded: chain O residue 645 HIS Chi-restraints excluded: chain O residue 648 ILE Chi-restraints excluded: chain O residue 654 ASP Chi-restraints excluded: chain O residue 710 ILE Chi-restraints excluded: chain O residue 721 TYR Chi-restraints excluded: chain O residue 751 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 495 GLN Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain X residue 271 VAL Chi-restraints excluded: chain X residue 272 ASP Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 522 VAL Chi-restraints excluded: chain X residue 529 MET Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 188 SER Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 293 LYS Chi-restraints excluded: chain Y residue 330 ARG Chi-restraints excluded: chain Y residue 354 ARG Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 408 ASP Chi-restraints excluded: chain Y residue 414 ILE Chi-restraints excluded: chain Y residue 496 ILE Chi-restraints excluded: chain Y residue 530 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 478 optimal weight: 0.0470 chunk 308 optimal weight: 8.9990 chunk 461 optimal weight: 0.6980 chunk 232 optimal weight: 7.9990 chunk 151 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 491 optimal weight: 0.7980 chunk 526 optimal weight: 4.9990 chunk 382 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 607 optimal weight: 9.9990 overall best weight: 2.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1359 ASN ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 663 GLN ** N 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 441 GLN ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 177 ASN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 65197 Z= 0.231 Angle : 0.653 17.977 88353 Z= 0.328 Chirality : 0.040 0.350 9963 Planarity : 0.004 0.078 11210 Dihedral : 7.481 63.266 9105 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.74 % Favored : 93.20 % Rotamer: Outliers : 5.45 % Allowed : 19.41 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.10), residues: 7998 helix: 1.55 (0.07), residues: 5446 sheet: -0.86 (0.25), residues: 394 loop : -2.40 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 752 HIS 0.009 0.001 HIS I 102 PHE 0.019 0.001 PHE N 713 TYR 0.052 0.001 TYR Y 100 ARG 0.016 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 366 poor density : 475 time to evaluate : 5.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 SER cc_start: 0.7214 (p) cc_final: 0.6704 (p) REVERT: A 485 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8456 (tp) REVERT: A 804 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8570 (t0) REVERT: A 945 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: A 1110 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8406 (mmp80) REVERT: A 1181 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9349 (mm) REVERT: A 1325 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9246 (mm) REVERT: A 1550 MET cc_start: 0.8373 (tpp) cc_final: 0.7765 (tpp) REVERT: A 1805 MET cc_start: 0.7827 (tpp) cc_final: 0.6764 (mmt) REVERT: A 1810 GLU cc_start: 0.8285 (mp0) cc_final: 0.7595 (mp0) REVERT: A 1911 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7160 (p90) REVERT: B 14 TRP cc_start: 0.5640 (OUTLIER) cc_final: 0.4272 (p-90) REVERT: C 232 PHE cc_start: 0.9659 (OUTLIER) cc_final: 0.9040 (m-80) REVERT: C 373 HIS cc_start: 0.7736 (t-170) cc_final: 0.7410 (t-170) REVERT: C 376 MET cc_start: 0.8975 (ttp) cc_final: 0.8721 (ttm) REVERT: E 73 ASP cc_start: 0.8274 (m-30) cc_final: 0.8037 (m-30) REVERT: F 154 SER cc_start: 0.9410 (OUTLIER) cc_final: 0.9054 (p) REVERT: F 463 MET cc_start: 0.8577 (tpt) cc_final: 0.8242 (tpp) REVERT: F 656 MET cc_start: 0.8646 (mtm) cc_final: 0.8294 (ptp) REVERT: H 71 CYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8755 (t) REVERT: H 611 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.8243 (m-10) REVERT: H 667 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8127 (pp30) REVERT: H 729 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9055 (tt) REVERT: I 64 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8750 (p) REVERT: I 250 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8594 (ptp-170) REVERT: I 305 MET cc_start: 0.8915 (mmm) cc_final: 0.8643 (mmt) REVERT: I 310 TRP cc_start: 0.8845 (OUTLIER) cc_final: 0.8245 (m100) REVERT: I 341 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8410 (t80) REVERT: I 647 GLU cc_start: 0.9564 (mt-10) cc_final: 0.9257 (tm-30) REVERT: I 717 MET cc_start: 0.6953 (tpt) cc_final: 0.6469 (tpt) REVERT: J 239 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8055 (mt-10) REVERT: J 354 MET cc_start: 0.8606 (mmt) cc_final: 0.8207 (mmm) REVERT: J 407 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8681 (mm-30) REVERT: J 437 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.7877 (t0) REVERT: J 497 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8370 (p0) REVERT: K 175 MET cc_start: 0.7841 (mtm) cc_final: 0.7504 (mtm) REVERT: K 193 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7101 (mt) REVERT: K 249 MET cc_start: 0.9020 (tpp) cc_final: 0.8767 (tpp) REVERT: K 351 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7057 (p0) REVERT: K 354 MET cc_start: 0.8857 (ttm) cc_final: 0.8003 (ttt) REVERT: K 371 MET cc_start: 0.8730 (mtp) cc_final: 0.8325 (ttp) REVERT: K 378 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.8227 (m-10) REVERT: L 12 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8547 (t0) REVERT: L 77 LEU cc_start: 0.9578 (tt) cc_final: 0.9363 (tp) REVERT: L 154 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7025 (mmp-170) REVERT: M 10 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7619 (pmm150) REVERT: M 52 GLU cc_start: 0.8909 (pt0) cc_final: 0.8655 (pp20) REVERT: M 54 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8511 (mt-10) REVERT: N 123 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: N 135 TRP cc_start: 0.8323 (OUTLIER) cc_final: 0.7973 (m-90) REVERT: N 172 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8684 (mpp) REVERT: N 383 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8473 (mp0) REVERT: N 387 LEU cc_start: 0.8821 (mt) cc_final: 0.8307 (mt) REVERT: N 431 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6407 (tpm170) REVERT: N 533 PHE cc_start: 0.5629 (OUTLIER) cc_final: 0.4366 (m-80) REVERT: N 622 TYR cc_start: 0.4153 (OUTLIER) cc_final: 0.3205 (t80) REVERT: N 646 MET cc_start: 0.3054 (tmm) cc_final: 0.2531 (mmm) REVERT: O 57 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8654 (ttp80) REVERT: O 264 VAL cc_start: 0.9389 (OUTLIER) cc_final: 0.9183 (p) REVERT: O 403 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.7025 (pptt) REVERT: O 408 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9070 (mt) REVERT: O 462 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.7999 (m-40) REVERT: O 508 MET cc_start: 0.8320 (mtt) cc_final: 0.8017 (mtm) REVERT: O 512 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.8830 (mp10) REVERT: P 119 MET cc_start: 0.9020 (tpp) cc_final: 0.8696 (tpp) REVERT: P 173 TYR cc_start: 0.8766 (t80) cc_final: 0.8479 (t80) REVERT: P 182 LEU cc_start: 0.9549 (mt) cc_final: 0.9329 (mt) REVERT: P 307 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9057 (mp) REVERT: P 365 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8446 (pp) REVERT: P 523 CYS cc_start: 0.7032 (t) cc_final: 0.6806 (p) REVERT: W 14 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.6729 (t0) REVERT: X 174 MET cc_start: 0.9031 (tpp) cc_final: 0.8792 (tpp) REVERT: X 304 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6190 (pp) REVERT: X 383 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8897 (tt) REVERT: X 386 MET cc_start: 0.8863 (mmm) cc_final: 0.8576 (mmm) REVERT: X 395 HIS cc_start: 0.8236 (m-70) cc_final: 0.7863 (m170) REVERT: X 447 LEU cc_start: 0.8892 (mt) cc_final: 0.8509 (tp) REVERT: Y 100 TYR cc_start: 0.7474 (m-80) cc_final: 0.7189 (m-80) REVERT: Y 262 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: Y 293 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8999 (tppt) REVERT: Y 295 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7652 (mp0) REVERT: Y 308 MET cc_start: 0.8979 (mmp) cc_final: 0.8476 (mmp) REVERT: Y 322 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8800 (mp0) REVERT: Y 330 ARG cc_start: 0.9407 (OUTLIER) cc_final: 0.8815 (ttp80) REVERT: Y 386 MET cc_start: 0.9060 (mmm) cc_final: 0.8829 (mmm) REVERT: Y 414 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8376 (mm) outliers start: 366 outliers final: 274 residues processed: 792 average time/residue: 0.6164 time to fit residues: 850.8240 Evaluate side-chains 769 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 446 time to evaluate : 5.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1024 MET Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1036 ASP Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1110 ARG Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1417 ASP Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1496 MET Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1507 THR Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1546 THR Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1611 VAL Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1641 THR Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1694 ASP Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain A residue 1911 PHE Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 536 CYS Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 481 CYS Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 487 ILE Chi-restraints excluded: chain F residue 494 HIS Chi-restraints excluded: chain F residue 607 LEU Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 634 HIS Chi-restraints excluded: chain F residue 673 CYS Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 480 ASN Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 530 ASN Chi-restraints excluded: chain H residue 563 ASP Chi-restraints excluded: chain H residue 611 PHE Chi-restraints excluded: chain H residue 612 VAL Chi-restraints excluded: chain H residue 667 GLN Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 250 ARG Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 284 ASP Chi-restraints excluded: chain I residue 310 TRP Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 328 LYS Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 350 SER Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 505 SER Chi-restraints excluded: chain I residue 656 THR Chi-restraints excluded: chain I residue 663 ASP Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 385 LYS Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 407 GLU Chi-restraints excluded: chain J residue 437 ASN Chi-restraints excluded: chain J residue 439 VAL Chi-restraints excluded: chain J residue 497 ASN Chi-restraints excluded: chain J residue 506 LEU Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 307 CYS Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 311 MET Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 438 GLU Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain K residue 442 ASP Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 144 ASN Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain L residue 154 ARG Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 135 TRP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 172 MET Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 371 ARG Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 378 LEU Chi-restraints excluded: chain N residue 383 GLU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 392 ASN Chi-restraints excluded: chain N residue 409 VAL Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 431 ARG Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 500 ASP Chi-restraints excluded: chain N residue 533 PHE Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 549 PHE Chi-restraints excluded: chain N residue 564 MET Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 624 LYS Chi-restraints excluded: chain N residue 649 GLU Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain N residue 768 LEU Chi-restraints excluded: chain N residue 773 ILE Chi-restraints excluded: chain N residue 814 VAL Chi-restraints excluded: chain N residue 817 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain O residue 138 HIS Chi-restraints excluded: chain O residue 250 PHE Chi-restraints excluded: chain O residue 257 SER Chi-restraints excluded: chain O residue 264 VAL Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 296 TYR Chi-restraints excluded: chain O residue 357 SER Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 369 VAL Chi-restraints excluded: chain O residue 370 HIS Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 462 ASN Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 512 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 550 VAL Chi-restraints excluded: chain O residue 567 LEU Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 641 LEU Chi-restraints excluded: chain O residue 645 HIS Chi-restraints excluded: chain O residue 648 ILE Chi-restraints excluded: chain O residue 654 ASP Chi-restraints excluded: chain O residue 704 VAL Chi-restraints excluded: chain O residue 706 CYS Chi-restraints excluded: chain O residue 710 ILE Chi-restraints excluded: chain O residue 721 TYR Chi-restraints excluded: chain O residue 751 LEU Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 432 ASP Chi-restraints excluded: chain P residue 495 GLN Chi-restraints excluded: chain P residue 536 CYS Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain X residue 271 VAL Chi-restraints excluded: chain X residue 272 ASP Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 505 ASN Chi-restraints excluded: chain X residue 522 VAL Chi-restraints excluded: chain X residue 529 MET Chi-restraints excluded: chain X residue 530 ASP Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 188 SER Chi-restraints excluded: chain Y residue 262 GLU Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 293 LYS Chi-restraints excluded: chain Y residue 330 ARG Chi-restraints excluded: chain Y residue 354 ARG Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 408 ASP Chi-restraints excluded: chain Y residue 414 ILE Chi-restraints excluded: chain Y residue 496 ILE Chi-restraints excluded: chain Y residue 530 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 703 optimal weight: 2.9990 chunk 740 optimal weight: 8.9990 chunk 675 optimal weight: 8.9990 chunk 720 optimal weight: 20.0000 chunk 433 optimal weight: 0.9990 chunk 313 optimal weight: 2.9990 chunk 565 optimal weight: 0.0170 chunk 221 optimal weight: 7.9990 chunk 650 optimal weight: 6.9990 chunk 681 optimal weight: 3.9990 chunk 717 optimal weight: 9.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1359 ASN A1380 ASN ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 413 ASN ** I 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 GLN ** J 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 65197 Z= 0.217 Angle : 0.656 17.338 88353 Z= 0.328 Chirality : 0.040 0.298 9963 Planarity : 0.004 0.051 11210 Dihedral : 7.360 59.808 9093 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.69 % Favored : 93.25 % Rotamer: Outliers : 5.24 % Allowed : 19.68 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.10), residues: 7998 helix: 1.60 (0.07), residues: 5446 sheet: -0.83 (0.25), residues: 389 loop : -2.37 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 752 HIS 0.007 0.001 HIS I 102 PHE 0.018 0.001 PHE X 294 TYR 0.051 0.001 TYR Y 100 ARG 0.014 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 352 poor density : 460 time to evaluate : 5.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8431 (tp) REVERT: A 804 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8563 (t0) REVERT: A 945 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: A 1110 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8402 (mmp80) REVERT: A 1181 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9349 (mm) REVERT: A 1279 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8107 (tpt90) REVERT: A 1325 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9236 (mm) REVERT: A 1380 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8199 (t0) REVERT: A 1550 MET cc_start: 0.8394 (tpp) cc_final: 0.7806 (tpp) REVERT: A 1805 MET cc_start: 0.7823 (tpp) cc_final: 0.6623 (mmt) REVERT: A 1810 GLU cc_start: 0.8289 (mp0) cc_final: 0.7533 (mp0) REVERT: A 1911 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7126 (p90) REVERT: B 14 TRP cc_start: 0.5635 (OUTLIER) cc_final: 0.4259 (p-90) REVERT: C 232 PHE cc_start: 0.9669 (OUTLIER) cc_final: 0.9131 (m-80) REVERT: E 71 LYS cc_start: 0.9351 (mmmt) cc_final: 0.9066 (mmmm) REVERT: E 73 ASP cc_start: 0.8299 (m-30) cc_final: 0.8056 (m-30) REVERT: F 154 SER cc_start: 0.9397 (OUTLIER) cc_final: 0.9035 (p) REVERT: F 656 MET cc_start: 0.8700 (mtm) cc_final: 0.8401 (ptp) REVERT: H 71 CYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8739 (t) REVERT: H 463 MET cc_start: 0.8856 (tmm) cc_final: 0.8418 (tmm) REVERT: H 611 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8259 (m-10) REVERT: H 667 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8112 (pp30) REVERT: H 729 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9061 (tt) REVERT: I 64 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8761 (p) REVERT: I 250 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8571 (ptp-170) REVERT: I 305 MET cc_start: 0.8932 (mmm) cc_final: 0.8678 (mmt) REVERT: I 310 TRP cc_start: 0.8808 (OUTLIER) cc_final: 0.8324 (m100) REVERT: I 341 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.8391 (t80) REVERT: I 647 GLU cc_start: 0.9566 (mt-10) cc_final: 0.9250 (tm-30) REVERT: I 717 MET cc_start: 0.6908 (tpt) cc_final: 0.6347 (tpt) REVERT: J 239 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8046 (mt-10) REVERT: J 354 MET cc_start: 0.8604 (mmt) cc_final: 0.8227 (mmm) REVERT: J 407 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8671 (mm-30) REVERT: J 437 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7866 (t0) REVERT: J 497 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8307 (p0) REVERT: K 63 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8221 (mtt-85) REVERT: K 175 MET cc_start: 0.7822 (mtm) cc_final: 0.7523 (mtm) REVERT: K 193 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7038 (mt) REVERT: K 249 MET cc_start: 0.9029 (tpp) cc_final: 0.8776 (tpp) REVERT: K 351 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7027 (p0) REVERT: K 354 MET cc_start: 0.8855 (ttm) cc_final: 0.8023 (ttt) REVERT: K 378 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8188 (m-10) REVERT: K 405 MET cc_start: 0.8403 (ptp) cc_final: 0.8188 (mtm) REVERT: L 12 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8527 (t0) REVERT: M 10 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7619 (pmm150) REVERT: M 51 LYS cc_start: 0.9095 (ttmt) cc_final: 0.8735 (tmtt) REVERT: M 52 GLU cc_start: 0.8912 (pt0) cc_final: 0.8579 (pp20) REVERT: M 54 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8532 (mt-10) REVERT: N 112 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8657 (pp) REVERT: N 135 TRP cc_start: 0.8318 (OUTLIER) cc_final: 0.7987 (m-90) REVERT: N 172 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8683 (mpp) REVERT: N 383 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8482 (mp0) REVERT: N 387 LEU cc_start: 0.8798 (mt) cc_final: 0.8286 (mt) REVERT: N 431 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6343 (tpm170) REVERT: N 533 PHE cc_start: 0.5571 (OUTLIER) cc_final: 0.4273 (m-80) REVERT: N 622 TYR cc_start: 0.4145 (OUTLIER) cc_final: 0.3197 (t80) REVERT: N 646 MET cc_start: 0.3117 (tmm) cc_final: 0.2549 (mmm) REVERT: O 57 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8678 (ttp80) REVERT: O 264 VAL cc_start: 0.9381 (OUTLIER) cc_final: 0.9175 (p) REVERT: O 408 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9005 (mt) REVERT: O 462 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8039 (m-40) REVERT: O 508 MET cc_start: 0.8322 (mtt) cc_final: 0.8066 (mtm) REVERT: O 512 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8883 (mp10) REVERT: P 119 MET cc_start: 0.8987 (tpp) cc_final: 0.8670 (tpp) REVERT: P 173 TYR cc_start: 0.8776 (t80) cc_final: 0.8480 (t80) REVERT: P 182 LEU cc_start: 0.9555 (mt) cc_final: 0.9284 (tp) REVERT: P 307 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9071 (mp) REVERT: P 365 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8431 (pp) REVERT: P 523 CYS cc_start: 0.6995 (t) cc_final: 0.6742 (p) REVERT: W 14 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.6747 (t0) REVERT: X 174 MET cc_start: 0.9030 (tpp) cc_final: 0.8792 (tpp) REVERT: X 304 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6052 (pp) REVERT: X 383 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8882 (tt) REVERT: X 386 MET cc_start: 0.8878 (mmm) cc_final: 0.8581 (mmm) REVERT: X 395 HIS cc_start: 0.8247 (m-70) cc_final: 0.7846 (m170) REVERT: X 447 LEU cc_start: 0.8810 (mt) cc_final: 0.8441 (tp) REVERT: Y 100 TYR cc_start: 0.7558 (m-80) cc_final: 0.7014 (m-80) REVERT: Y 262 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: Y 293 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8987 (tppt) REVERT: Y 295 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7589 (mp0) REVERT: Y 299 MET cc_start: 0.9040 (mtt) cc_final: 0.8702 (mtp) REVERT: Y 308 MET cc_start: 0.8946 (mmp) cc_final: 0.8443 (mmp) REVERT: Y 322 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8732 (pm20) REVERT: Y 330 ARG cc_start: 0.9410 (OUTLIER) cc_final: 0.8806 (ttp80) REVERT: Y 386 MET cc_start: 0.9094 (mmm) cc_final: 0.8866 (mmm) REVERT: Y 414 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8366 (mm) outliers start: 352 outliers final: 273 residues processed: 768 average time/residue: 0.5878 time to fit residues: 788.1647 Evaluate side-chains 764 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 441 time to evaluate : 5.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1024 MET Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1086 MET Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1110 ARG Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1417 ASP Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1496 MET Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1507 THR Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1546 THR Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1641 THR Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1694 ASP Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain A residue 1911 PHE Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 536 CYS Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 481 CYS Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 487 ILE Chi-restraints excluded: chain F residue 494 HIS Chi-restraints excluded: chain F residue 523 SER Chi-restraints excluded: chain F residue 607 LEU Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 634 HIS Chi-restraints excluded: chain F residue 673 CYS Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 480 ASN Chi-restraints excluded: chain H residue 530 ASN Chi-restraints excluded: chain H residue 563 ASP Chi-restraints excluded: chain H residue 611 PHE Chi-restraints excluded: chain H residue 667 GLN Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 250 ARG Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 284 ASP Chi-restraints excluded: chain I residue 310 TRP Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 328 LYS Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 350 SER Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 505 SER Chi-restraints excluded: chain I residue 559 ASP Chi-restraints excluded: chain I residue 656 THR Chi-restraints excluded: chain I residue 663 ASP Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 407 GLU Chi-restraints excluded: chain J residue 437 ASN Chi-restraints excluded: chain J residue 439 VAL Chi-restraints excluded: chain J residue 497 ASN Chi-restraints excluded: chain J residue 506 LEU Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 307 CYS Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 311 MET Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 438 GLU Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 144 ASN Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain L residue 154 ARG Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 135 TRP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 172 MET Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 371 ARG Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 378 LEU Chi-restraints excluded: chain N residue 383 GLU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 392 ASN Chi-restraints excluded: chain N residue 409 VAL Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 431 ARG Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 500 ASP Chi-restraints excluded: chain N residue 533 PHE Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 564 MET Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 624 LYS Chi-restraints excluded: chain N residue 649 GLU Chi-restraints excluded: chain N residue 650 LEU Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain N residue 768 LEU Chi-restraints excluded: chain N residue 773 ILE Chi-restraints excluded: chain N residue 814 VAL Chi-restraints excluded: chain N residue 817 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain O residue 138 HIS Chi-restraints excluded: chain O residue 250 PHE Chi-restraints excluded: chain O residue 257 SER Chi-restraints excluded: chain O residue 264 VAL Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 296 TYR Chi-restraints excluded: chain O residue 357 SER Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 369 VAL Chi-restraints excluded: chain O residue 370 HIS Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 462 ASN Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 512 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 550 VAL Chi-restraints excluded: chain O residue 567 LEU Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 645 HIS Chi-restraints excluded: chain O residue 654 ASP Chi-restraints excluded: chain O residue 706 CYS Chi-restraints excluded: chain O residue 710 ILE Chi-restraints excluded: chain O residue 721 TYR Chi-restraints excluded: chain O residue 751 LEU Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 432 ASP Chi-restraints excluded: chain P residue 495 GLN Chi-restraints excluded: chain P residue 536 CYS Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain X residue 271 VAL Chi-restraints excluded: chain X residue 272 ASP Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 522 VAL Chi-restraints excluded: chain X residue 529 MET Chi-restraints excluded: chain X residue 530 ASP Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 172 ASN Chi-restraints excluded: chain Y residue 188 SER Chi-restraints excluded: chain Y residue 262 GLU Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 293 LYS Chi-restraints excluded: chain Y residue 330 ARG Chi-restraints excluded: chain Y residue 354 ARG Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 408 ASP Chi-restraints excluded: chain Y residue 414 ILE Chi-restraints excluded: chain Y residue 496 ILE Chi-restraints excluded: chain Y residue 530 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 473 optimal weight: 3.9990 chunk 761 optimal weight: 7.9990 chunk 464 optimal weight: 0.0070 chunk 361 optimal weight: 6.9990 chunk 529 optimal weight: 6.9990 chunk 798 optimal weight: 20.0000 chunk 735 optimal weight: 5.9990 chunk 636 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 491 optimal weight: 3.9990 chunk 390 optimal weight: 7.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1359 ASN A1380 ASN ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 241 HIS ** J 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.268 65197 Z= 0.282 Angle : 0.723 59.195 88353 Z= 0.375 Chirality : 0.042 0.812 9963 Planarity : 0.004 0.079 11210 Dihedral : 7.343 59.804 9089 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.72 % Favored : 93.22 % Rotamer: Outliers : 5.14 % Allowed : 19.83 % Favored : 75.03 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.10), residues: 7998 helix: 1.59 (0.07), residues: 5446 sheet: -0.83 (0.25), residues: 389 loop : -2.37 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 752 HIS 0.011 0.001 HIS C 373 PHE 0.020 0.001 PHE E 105 TYR 0.049 0.001 TYR Y 100 ARG 0.025 0.000 ARG H 532 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15996 Ramachandran restraints generated. 7998 Oldfield, 0 Emsley, 7998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 442 time to evaluate : 6.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8433 (tp) REVERT: A 804 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8566 (t0) REVERT: A 945 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8101 (mp0) REVERT: A 1110 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8401 (mmp80) REVERT: A 1181 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9349 (mm) REVERT: A 1279 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8107 (tpt90) REVERT: A 1325 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9231 (mm) REVERT: A 1550 MET cc_start: 0.8394 (tpp) cc_final: 0.7806 (tpp) REVERT: A 1805 MET cc_start: 0.7818 (tpp) cc_final: 0.6617 (mmt) REVERT: A 1810 GLU cc_start: 0.8289 (mp0) cc_final: 0.7527 (mp0) REVERT: A 1911 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7144 (p90) REVERT: B 14 TRP cc_start: 0.5629 (OUTLIER) cc_final: 0.4258 (p-90) REVERT: C 160 LYS cc_start: 0.9492 (OUTLIER) cc_final: 0.9110 (tppt) REVERT: C 232 PHE cc_start: 0.9665 (OUTLIER) cc_final: 0.9129 (m-80) REVERT: E 73 ASP cc_start: 0.8300 (m-30) cc_final: 0.8046 (m-30) REVERT: F 154 SER cc_start: 0.9398 (OUTLIER) cc_final: 0.9035 (p) REVERT: F 656 MET cc_start: 0.8702 (mtm) cc_final: 0.8400 (ptp) REVERT: H 71 CYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8737 (t) REVERT: H 463 MET cc_start: 0.8855 (tmm) cc_final: 0.8409 (tmm) REVERT: H 611 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8270 (m-10) REVERT: H 667 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8113 (pp30) REVERT: H 729 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9062 (tt) REVERT: I 64 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8766 (p) REVERT: I 250 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8578 (ptp-170) REVERT: I 305 MET cc_start: 0.8934 (mmm) cc_final: 0.8679 (mmt) REVERT: I 310 TRP cc_start: 0.8815 (OUTLIER) cc_final: 0.8322 (m100) REVERT: I 341 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.8388 (t80) REVERT: I 647 GLU cc_start: 0.9567 (mt-10) cc_final: 0.9250 (tm-30) REVERT: I 717 MET cc_start: 0.6913 (tpt) cc_final: 0.6349 (tpt) REVERT: J 239 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8049 (mt-10) REVERT: J 354 MET cc_start: 0.8608 (mmt) cc_final: 0.8227 (mmm) REVERT: J 407 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8655 (mm-30) REVERT: J 437 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.7866 (t0) REVERT: J 497 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8298 (p0) REVERT: K 63 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8218 (mtt-85) REVERT: K 175 MET cc_start: 0.7834 (mtm) cc_final: 0.7515 (mtm) REVERT: K 193 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7039 (mt) REVERT: K 249 MET cc_start: 0.9028 (tpp) cc_final: 0.8775 (tpp) REVERT: K 351 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7027 (p0) REVERT: K 354 MET cc_start: 0.8851 (ttm) cc_final: 0.8025 (ttt) REVERT: K 378 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8189 (m-10) REVERT: K 405 MET cc_start: 0.8396 (ptp) cc_final: 0.8190 (mtm) REVERT: L 12 ASP cc_start: 0.9149 (OUTLIER) cc_final: 0.8538 (t0) REVERT: M 10 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7609 (pmm150) REVERT: M 51 LYS cc_start: 0.9095 (ttmt) cc_final: 0.8736 (tmtt) REVERT: M 52 GLU cc_start: 0.8908 (pt0) cc_final: 0.8582 (pp20) REVERT: M 54 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8529 (mt-10) REVERT: N 112 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8657 (pp) REVERT: N 135 TRP cc_start: 0.8313 (OUTLIER) cc_final: 0.7978 (m-90) REVERT: N 172 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8684 (mpp) REVERT: N 383 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8482 (mp0) REVERT: N 387 LEU cc_start: 0.8799 (mt) cc_final: 0.8286 (mt) REVERT: N 431 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6342 (tpm170) REVERT: N 533 PHE cc_start: 0.5569 (OUTLIER) cc_final: 0.4273 (m-80) REVERT: N 622 TYR cc_start: 0.4141 (OUTLIER) cc_final: 0.3193 (t80) REVERT: N 646 MET cc_start: 0.3149 (tmm) cc_final: 0.2561 (mmm) REVERT: O 57 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8677 (ttp80) REVERT: O 264 VAL cc_start: 0.9382 (OUTLIER) cc_final: 0.9176 (p) REVERT: O 408 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9002 (mt) REVERT: O 462 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8039 (m-40) REVERT: O 508 MET cc_start: 0.8322 (mtt) cc_final: 0.8056 (mtm) REVERT: O 512 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8857 (mp10) REVERT: P 119 MET cc_start: 0.8986 (tpp) cc_final: 0.8671 (tpp) REVERT: P 173 TYR cc_start: 0.8777 (t80) cc_final: 0.8482 (t80) REVERT: P 182 LEU cc_start: 0.9555 (mt) cc_final: 0.9281 (tp) REVERT: P 307 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9066 (mp) REVERT: P 365 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8432 (pp) REVERT: P 523 CYS cc_start: 0.6995 (t) cc_final: 0.6742 (p) REVERT: W 14 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.6754 (t0) REVERT: X 174 MET cc_start: 0.9029 (tpp) cc_final: 0.8794 (tpp) REVERT: X 304 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6049 (pp) REVERT: X 383 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8883 (tt) REVERT: X 386 MET cc_start: 0.8876 (mmm) cc_final: 0.8582 (mmm) REVERT: X 395 HIS cc_start: 0.8244 (m-70) cc_final: 0.7846 (m170) REVERT: X 447 LEU cc_start: 0.8800 (mt) cc_final: 0.8440 (tp) REVERT: Y 100 TYR cc_start: 0.7547 (m-80) cc_final: 0.6999 (m-80) REVERT: Y 262 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: Y 293 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8988 (tppt) REVERT: Y 295 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7586 (mp0) REVERT: Y 299 MET cc_start: 0.9037 (mtt) cc_final: 0.8702 (mtp) REVERT: Y 308 MET cc_start: 0.8952 (mmp) cc_final: 0.8384 (mmp) REVERT: Y 322 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8730 (pm20) REVERT: Y 330 ARG cc_start: 0.9413 (OUTLIER) cc_final: 0.8810 (ttp80) REVERT: Y 386 MET cc_start: 0.9096 (mmm) cc_final: 0.8866 (mmm) REVERT: Y 414 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8367 (mm) outliers start: 345 outliers final: 283 residues processed: 739 average time/residue: 0.5828 time to fit residues: 752.4255 Evaluate side-chains 771 residues out of total 7111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 438 time to evaluate : 5.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1024 MET Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1086 MET Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1110 ARG Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1417 ASP Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1496 MET Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1507 THR Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1546 THR Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1641 THR Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1694 ASP Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain A residue 1911 PHE Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 536 CYS Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 481 CYS Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 487 ILE Chi-restraints excluded: chain F residue 494 HIS Chi-restraints excluded: chain F residue 607 LEU Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 634 HIS Chi-restraints excluded: chain F residue 673 CYS Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 480 ASN Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 530 ASN Chi-restraints excluded: chain H residue 563 ASP Chi-restraints excluded: chain H residue 611 PHE Chi-restraints excluded: chain H residue 667 GLN Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 250 ARG Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 284 ASP Chi-restraints excluded: chain I residue 310 TRP Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 328 LYS Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 350 SER Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 505 SER Chi-restraints excluded: chain I residue 559 ASP Chi-restraints excluded: chain I residue 656 THR Chi-restraints excluded: chain I residue 663 ASP Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 258 MET Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 407 GLU Chi-restraints excluded: chain J residue 437 ASN Chi-restraints excluded: chain J residue 439 VAL Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 497 ASN Chi-restraints excluded: chain J residue 506 LEU Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 307 CYS Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 311 MET Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 438 GLU Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 144 ASN Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain L residue 154 ARG Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 135 TRP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 172 MET Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 371 ARG Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 378 LEU Chi-restraints excluded: chain N residue 383 GLU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 392 ASN Chi-restraints excluded: chain N residue 409 VAL Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 417 LEU Chi-restraints excluded: chain N residue 431 ARG Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 500 ASP Chi-restraints excluded: chain N residue 533 PHE Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 564 MET Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 624 LYS Chi-restraints excluded: chain N residue 649 GLU Chi-restraints excluded: chain N residue 650 LEU Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain N residue 768 LEU Chi-restraints excluded: chain N residue 773 ILE Chi-restraints excluded: chain N residue 814 VAL Chi-restraints excluded: chain N residue 817 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain O residue 138 HIS Chi-restraints excluded: chain O residue 250 PHE Chi-restraints excluded: chain O residue 257 SER Chi-restraints excluded: chain O residue 264 VAL Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 296 TYR Chi-restraints excluded: chain O residue 357 SER Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 369 VAL Chi-restraints excluded: chain O residue 370 HIS Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 462 ASN Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 512 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 550 VAL Chi-restraints excluded: chain O residue 567 LEU Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 641 LEU Chi-restraints excluded: chain O residue 645 HIS Chi-restraints excluded: chain O residue 654 ASP Chi-restraints excluded: chain O residue 678 TYR Chi-restraints excluded: chain O residue 706 CYS Chi-restraints excluded: chain O residue 710 ILE Chi-restraints excluded: chain O residue 721 TYR Chi-restraints excluded: chain O residue 751 LEU Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 432 ASP Chi-restraints excluded: chain P residue 495 GLN Chi-restraints excluded: chain P residue 536 CYS Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 148 MET Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain X residue 271 VAL Chi-restraints excluded: chain X residue 272 ASP Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 505 ASN Chi-restraints excluded: chain X residue 522 VAL Chi-restraints excluded: chain X residue 529 MET Chi-restraints excluded: chain X residue 530 ASP Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 172 ASN Chi-restraints excluded: chain Y residue 188 SER Chi-restraints excluded: chain Y residue 262 GLU Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 293 LYS Chi-restraints excluded: chain Y residue 330 ARG Chi-restraints excluded: chain Y residue 354 ARG Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 408 ASP Chi-restraints excluded: chain Y residue 414 ILE Chi-restraints excluded: chain Y residue 496 ILE Chi-restraints excluded: chain Y residue 530 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 505 optimal weight: 3.9990 chunk 677 optimal weight: 9.9990 chunk 194 optimal weight: 0.6980 chunk 586 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 637 optimal weight: 0.7980 chunk 266 optimal weight: 9.9990 chunk 654 optimal weight: 3.9990 chunk 80 optimal weight: 0.0000 chunk 117 optimal weight: 2.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1359 ASN ** A1380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.066382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.048399 restraints weight = 329141.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.049791 restraints weight = 165442.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.050687 restraints weight = 105441.271| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.268 65197 Z= 0.282 Angle : 0.723 59.195 88353 Z= 0.375 Chirality : 0.042 0.812 9963 Planarity : 0.004 0.079 11210 Dihedral : 7.341 59.804 9087 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.72 % Favored : 93.22 % Rotamer: Outliers : 4.97 % Allowed : 19.86 % Favored : 75.17 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.10), residues: 7998 helix: 1.59 (0.07), residues: 5446 sheet: -0.83 (0.25), residues: 389 loop : -2.37 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 752 HIS 0.011 0.001 HIS C 373 PHE 0.020 0.001 PHE E 105 TYR 0.049 0.001 TYR Y 100 ARG 0.025 0.000 ARG H 532 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14345.89 seconds wall clock time: 254 minutes 36.71 seconds (15276.71 seconds total)