Starting phenix.real_space_refine on Fri Jul 26 20:23:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6n_31743/07_2024/7v6n_31743.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6n_31743/07_2024/7v6n_31743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6n_31743/07_2024/7v6n_31743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6n_31743/07_2024/7v6n_31743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6n_31743/07_2024/7v6n_31743.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6n_31743/07_2024/7v6n_31743.cif" } resolution = 3.99 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= 0.002 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: 4 Type Number sf(0) Gaussians S 183 5.16 5 C 21700 2.51 5 N 5767 2.21 5 O 6798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 510": "OD1" <-> "OD2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 771": "OD1" <-> "OD2" Residue "A PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 823": "OE1" <-> "OE2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A ASP 896": "OD1" <-> "OD2" Residue "A GLU 1148": "OE1" <-> "OE2" Residue "B TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 174": "OD1" <-> "OD2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 510": "OD1" <-> "OD2" Residue "B PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 626": "NH1" <-> "NH2" Residue "B TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 680": "OE1" <-> "OE2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 844": "OD1" <-> "OD2" Residue "B ARG 887": "NH1" <-> "NH2" Residue "B TYR 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1183": "OE1" <-> "OE2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C GLU 357": "OE1" <-> "OE2" Residue "C GLU 376": "OE1" <-> "OE2" Residue "C GLU 382": "OE1" <-> "OE2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 444": "OD1" <-> "OD2" Residue "C PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 536": "OE1" <-> "OE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "C ARG 626": "NH1" <-> "NH2" Residue "C GLU 944": "OE1" <-> "OE2" Residue "C ASP 1059": "OD1" <-> "OD2" Residue "D TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 56": "NH1" <-> "NH2" Residue "D TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "F TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 56": "NH1" <-> "NH2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G ARG 67": "NH1" <-> "NH2" Residue "G ARG 87": "NH1" <-> "NH2" Residue "G ARG 98": "NH1" <-> "NH2" Residue "G TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 56": "NH1" <-> "NH2" Residue "H TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 218": "OE1" <-> "OE2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I ARG 67": "NH1" <-> "NH2" Residue "I ASP 73": "OD1" <-> "OD2" Residue "I ARG 87": "NH1" <-> "NH2" Residue "I ARG 98": "NH1" <-> "NH2" Residue "I TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.83s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 34448 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1135, 8343 Classifications: {'peptide': 1135} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 49, 'TRANS': 1085} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 6, 'TYR:plan': 13, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 14, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 343 Chain: "B" Number of atoms: 8184 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1102, 8178 Classifications: {'peptide': 1102} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 45, 'TRANS': 1056} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 397 Unresolved non-hydrogen angles: 500 Unresolved non-hydrogen dihedrals: 350 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 10, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 8, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 282 Conformer: "B" Number of residues, atoms: 1102, 8178 Classifications: {'peptide': 1102} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 45, 'TRANS': 1056} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 397 Unresolved non-hydrogen angles: 500 Unresolved non-hydrogen dihedrals: 350 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 10, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 8, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 282 bond proxies already assigned to first conformer: 8337 Chain: "C" Number of atoms: 8029 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1097, 8023 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 48, 'TRANS': 1048} Chain breaks: 12 Unresolved non-hydrogen bonds: 505 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 7, 'TYR:plan': 10, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 13, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 348 Conformer: "B" Number of residues, atoms: 1097, 8023 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 48, 'TRANS': 1048} Chain breaks: 12 Unresolved non-hydrogen bonds: 505 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 7, 'TYR:plan': 10, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 13, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 348 bond proxies already assigned to first conformer: 8171 Chain: "D" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1623 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "E" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1658 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 215} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 3, 'TYR:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1637 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1700 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 215} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1622 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "I" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1652 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 11, 'TRANS': 215} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 58 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER B 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER B 51 " occ=0.54 residue: pdb=" N ASER C 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER C 51 " occ=0.54 Time building chain proxies: 24.95, per 1000 atoms: 0.72 Number of scatterers: 34448 At special positions: 0 Unit cell: (208.601, 220.678, 203.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 183 16.00 O 6798 8.00 N 5767 7.00 C 21700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.04 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.02 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.04 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.02 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.02 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.02 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.04 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.04 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.05 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.04 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.02 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.02 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 199 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 212 " distance=2.03 Simple disulfide: pdb=" SG CYS F 26 " - pdb=" SG CYS F 91 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 156 " - pdb=" SG CYS G 212 " distance=2.03 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 199 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 156 " - pdb=" SG CYS I 212 " 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: 12.19 Conformation dependent library (CDL) restraints added in 9.0 seconds 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8682 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 71 sheets defined 18.7% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 220 through 231 removed outlier: 4.114A pdb=" N SER A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 342 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 410 through 418 Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.848A pdb=" N SER A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 529 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.561A pdb=" N ASN A 812 " --> pdb=" O TYR A 809 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY A 813 " --> pdb=" O VAL A 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 809 through 813' Processing helix chain 'A' and resid 814 through 823 removed outlier: 4.156A pdb=" N GLU A 823 " --> pdb=" O GLN A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 852 removed outlier: 4.108A pdb=" N SER A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 915 Processing helix chain 'A' and resid 925 through 930 Processing helix chain 'A' and resid 940 through 959 removed outlier: 4.265A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 987 through 1011 removed outlier: 3.507A pdb=" N ASN A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1041 Processing helix chain 'A' and resid 1059 through 1106 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 268 through 273 removed outlier: 4.104A pdb=" N LEU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 410 through 418 Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 524 through 530 removed outlier: 4.095A pdb=" N SER B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 529 " --> pdb=" O PRO B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.669A pdb=" N TYR B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 854 removed outlier: 3.881A pdb=" N VAL B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 907 through 915 Processing helix chain 'B' and resid 940 through 954 Processing helix chain 'B' and resid 955 through 958 removed outlier: 3.768A pdb=" N VAL B 958 " --> pdb=" O ILE B 955 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 955 through 958' Processing helix chain 'B' and resid 971 through 984 Processing helix chain 'B' and resid 987 through 994 Processing helix chain 'B' and resid 996 through 1010 Processing helix chain 'B' and resid 1017 through 1041 removed outlier: 3.777A pdb=" N LYS B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1106 Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.640A pdb=" N PHE C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 268 through 273 removed outlier: 4.182A pdb=" N LEU C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 410 through 418 Processing helix chain 'C' and resid 429 through 436 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 530 removed outlier: 3.691A pdb=" N SER C 528 " --> pdb=" O SER C 524 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 529 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 824 through 854 Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 907 through 915 Processing helix chain 'C' and resid 925 through 930 Processing helix chain 'C' and resid 940 through 958 Processing helix chain 'C' and resid 975 through 982 Processing helix chain 'C' and resid 1005 through 1011 Processing helix chain 'C' and resid 1018 through 1041 removed outlier: 3.576A pdb=" N VAL C1022 " --> pdb=" O ALA C1018 " (cutoff:3.500A) Processing helix chain 'C' and resid 1059 through 1106 Processing helix chain 'D' and resid 126 through 133 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 144 through 149 removed outlier: 3.560A pdb=" N SER E 148 " --> pdb=" O SER E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'F' and resid 126 through 133 removed outlier: 3.547A pdb=" N LEU F 130 " --> pdb=" O SER F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 194 Processing helix chain 'G' and resid 144 through 149 removed outlier: 3.680A pdb=" N SER G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'H' and resid 126 through 133 Processing helix chain 'H' and resid 188 through 194 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 144 through 149 Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 3.679A pdb=" N VAL A 102 " --> pdb=" O ASP A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 75 removed outlier: 3.543A pdb=" N GLY A 73 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.783A pdb=" N TYR A 314 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 119 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 243 removed outlier: 7.615A pdb=" N ARG A 235 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLU A 188 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N CYS A 237 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE A 186 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A 239 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 184 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 206 through 208 removed outlier: 5.365A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 360 through 367 removed outlier: 5.490A pdb=" N SER A 362 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL A 661 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N SER A 364 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL A 659 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 671 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 400 through 404 removed outlier: 7.230A pdb=" N THR A 477 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N CYS A 425 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU A 479 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N PHE A 423 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 481 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.343A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 605 through 607 removed outlier: 3.858A pdb=" N GLY A 613 " --> pdb=" O TYR A 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 631 through 632 Processing sheet with id=AB3, first strand: chain 'A' and resid 779 through 781 Processing sheet with id=AB4, first strand: chain 'A' and resid 801 through 803 removed outlier: 4.585A pdb=" N LYS A 801 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1121 through 1128 removed outlier: 5.555A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AB7, first strand: chain 'B' and resid 69 through 75 removed outlier: 3.579A pdb=" N LEU B 325 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 73 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.676A pdb=" N ILE B 120 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 252 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.564A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.282A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.282A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.543A pdb=" N GLY B 128 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 138 " --> pdb=" O GLY B 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.829A pdb=" N TYR B 361 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 661 " --> pdb=" O TYR B 361 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 662 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B 671 " --> pdb=" O ILE B 662 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 375 through 376 removed outlier: 3.676A pdb=" N GLU B 376 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 400 through 405 removed outlier: 3.578A pdb=" N LYS B 400 " --> pdb=" O TYR B 445 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.161A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 631 through 632 Processing sheet with id=AC9, first strand: chain 'B' and resid 791 through 795 removed outlier: 3.614A pdb=" N THR B 791 " --> pdb=" O HIS B1138 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AD2, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AD3, first strand: chain 'C' and resid 69 through 76 removed outlier: 3.694A pdb=" N ILE C 69 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 282 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.644A pdb=" N LEU C 324 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AD6, first strand: chain 'C' and resid 232 through 244 removed outlier: 4.556A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS C 185 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 153 through 154 removed outlier: 3.554A pdb=" N ARG C 163 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 206 through 208 removed outlier: 5.491A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 359 through 367 removed outlier: 4.633A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C 672 " --> pdb=" O ASN C 719 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 400 through 405 removed outlier: 3.639A pdb=" N LYS C 400 " --> pdb=" O TYR C 445 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 408 through 409 Processing sheet with id=AE3, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.061A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 777 through 783 removed outlier: 3.507A pdb=" N LEU C 780 " --> pdb=" O VAL C1149 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 802 through 804 Processing sheet with id=AE6, first strand: chain 'C' and resid 1127 through 1130 Processing sheet with id=AE7, first strand: chain 'D' and resid 14 through 15 removed outlier: 6.161A pdb=" N LEU D 14 " --> pdb=" O GLU D 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 22 through 27 Processing sheet with id=AE9, first strand: chain 'D' and resid 48 through 51 removed outlier: 6.571A pdb=" N TRP D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR D 35 " --> pdb=" O SER D 94 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 119 through 123 Processing sheet with id=AF2, first strand: chain 'D' and resid 134 through 135 Processing sheet with id=AF3, first strand: chain 'D' and resid 158 through 160 removed outlier: 4.508A pdb=" N TRP D 153 " --> pdb=" O GLN D 160 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.666A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP E 73 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.336A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 136 through 140 removed outlier: 4.251A pdb=" N GLY E 155 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA E 152 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR E 192 " --> pdb=" O ASP E 160 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER E 193 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA E 184 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER E 195 " --> pdb=" O PHE E 182 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 166 through 170 removed outlier: 3.629A pdb=" N THR E 221 " --> pdb=" O HIS E 216 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 13 through 15 Processing sheet with id=AF9, first strand: chain 'F' and resid 22 through 26 Processing sheet with id=AG1, first strand: chain 'F' and resid 48 through 51 removed outlier: 6.640A pdb=" N TRP F 38 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 119 through 123 Processing sheet with id=AG3, first strand: chain 'F' and resid 158 through 160 removed outlier: 4.413A pdb=" N TRP F 153 " --> pdb=" O GLN F 160 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.782A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP G 73 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 58 through 60 removed outlier: 5.370A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 136 through 140 removed outlier: 3.783A pdb=" N GLY G 155 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA G 152 " --> pdb=" O VAL G 200 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP G 160 " --> pdb=" O TYR G 192 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR G 192 " --> pdb=" O ASP G 160 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 167 through 170 Processing sheet with id=AG8, first strand: chain 'H' and resid 8 through 9 removed outlier: 4.210A pdb=" N THR H 8 " --> pdb=" O ARG H 27 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 13 through 15 Processing sheet with id=AH1, first strand: chain 'H' and resid 48 through 51 removed outlier: 6.608A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR H 88 " --> pdb=" O GLN H 41 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 119 through 123 Processing sheet with id=AH3, first strand: chain 'H' and resid 134 through 135 Processing sheet with id=AH4, first strand: chain 'H' and resid 158 through 160 removed outlier: 4.554A pdb=" N TRP H 153 " --> pdb=" O GLN H 160 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.647A pdb=" N THR I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 58 through 60 removed outlier: 5.406A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 136 through 140 removed outlier: 4.313A pdb=" N GLY I 155 " --> pdb=" O LEU I 140 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP I 160 " --> pdb=" O TYR I 192 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR I 192 " --> pdb=" O ASP I 160 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 166 through 170 1227 hydrogen bonds defined for protein. 3312 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: 14.32 Time building geometry restraints manager: 13.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6638 1.33 - 1.45: 8722 1.45 - 1.58: 19566 1.58 - 1.70: 0 1.70 - 1.82: 233 Bond restraints: 35159 Sorted by residual: bond pdb=" N VAL A 657 " pdb=" CA VAL A 657 " ideal model delta sigma weight residual 1.460 1.497 -0.036 7.60e-03 1.73e+04 2.30e+01 bond pdb=" N ARG I 87 " pdb=" CA ARG I 87 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.89e+01 bond pdb=" N CYS B 195 " pdb=" CA CYS B 195 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.80e+01 bond pdb=" N ILE B 296 " pdb=" CA ILE B 296 " ideal model delta sigma weight residual 1.460 1.491 -0.031 7.50e-03 1.78e+04 1.76e+01 bond pdb=" N ILE C 782 " pdb=" CA ILE C 782 " ideal model delta sigma weight residual 1.457 1.495 -0.037 9.00e-03 1.23e+04 1.73e+01 ... (remaining 35154 not shown) Histogram of bond angle deviations from ideal: 96.48 - 104.07: 424 104.07 - 111.65: 14564 111.65 - 119.24: 17905 119.24 - 126.83: 14813 126.83 - 134.42: 226 Bond angle restraints: 47932 Sorted by residual: angle pdb=" C ASP B 510 " pdb=" CA ASP B 510 " pdb=" CB ASP B 510 " ideal model delta sigma weight residual 109.83 117.39 -7.56 9.90e-01 1.02e+00 5.83e+01 angle pdb=" N LEU B 600 " pdb=" CA LEU B 600 " pdb=" C LEU B 600 " ideal model delta sigma weight residual 114.56 105.99 8.57 1.27e+00 6.20e-01 4.55e+01 angle pdb=" N ALA B 930 " pdb=" CA ALA B 930 " pdb=" C ALA B 930 " ideal model delta sigma weight residual 110.80 96.48 14.32 2.13e+00 2.20e-01 4.52e+01 angle pdb=" N CYS A 603 " pdb=" CA CYS A 603 " pdb=" C CYS A 603 " ideal model delta sigma weight residual 108.41 118.37 -9.96 1.63e+00 3.76e-01 3.74e+01 angle pdb=" N ARG H 147 " pdb=" CA ARG H 147 " pdb=" C ARG H 147 " ideal model delta sigma weight residual 111.36 104.76 6.60 1.09e+00 8.42e-01 3.67e+01 ... (remaining 47927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 19005 16.83 - 33.67: 1345 33.67 - 50.50: 478 50.50 - 67.33: 120 67.33 - 84.17: 12 Dihedral angle restraints: 20960 sinusoidal: 7425 harmonic: 13535 Sorted by residual: dihedral pdb=" CB CYS F 26 " pdb=" SG CYS F 26 " pdb=" SG CYS F 91 " pdb=" CB CYS F 91 " ideal model delta sinusoidal sigma weight residual -86.00 -170.17 84.17 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS C 679 " pdb=" SG CYS C 679 " pdb=" SG CYS C 713 " pdb=" CB CYS C 713 " ideal model delta sinusoidal sigma weight residual -86.00 -157.98 71.98 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS A 620 " pdb=" SG CYS A 620 " pdb=" SG CYS A 650 " pdb=" CB CYS A 650 " ideal model delta sinusoidal sigma weight residual -86.00 -150.59 64.59 1 1.00e+01 1.00e-02 5.48e+01 ... (remaining 20957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3861 0.115 - 0.230: 1585 0.230 - 0.346: 101 0.346 - 0.461: 1 0.461 - 0.576: 2 Chirality restraints: 5550 Sorted by residual: chirality pdb=" CA ARG B1179 " pdb=" N ARG B1179 " pdb=" C ARG B1179 " pdb=" CB ARG B1179 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.29e+00 chirality pdb=" CA TYR C 641 " pdb=" N TYR C 641 " pdb=" C TYR C 641 " pdb=" CB TYR C 641 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.51 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" CA ASN F 143 " pdb=" N ASN F 143 " pdb=" C ASN F 143 " pdb=" CB ASN F 143 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.77e+00 ... (remaining 5547 not shown) Planarity restraints: 6205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BSER C 51 " -0.034 2.00e-02 2.50e+03 7.10e-02 5.04e+01 pdb=" C BSER C 51 " 0.123 2.00e-02 2.50e+03 pdb=" O BSER C 51 " -0.046 2.00e-02 2.50e+03 pdb=" N LYS C 52 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASER C 51 " -0.031 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C ASER C 51 " 0.110 2.00e-02 2.50e+03 pdb=" O ASER C 51 " -0.041 2.00e-02 2.50e+03 pdb=" N LYS C 52 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 50 " 0.030 2.00e-02 2.50e+03 6.11e-02 3.73e+01 pdb=" C VAL B 50 " -0.106 2.00e-02 2.50e+03 pdb=" O VAL B 50 " 0.039 2.00e-02 2.50e+03 pdb=" N BSER B 51 " 0.037 2.00e-02 2.50e+03 ... (remaining 6202 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.96: 7 1.96 - 2.70: 886 2.70 - 3.43: 47148 3.43 - 4.17: 85730 4.17 - 4.90: 141178 Nonbonded interactions: 274949 Sorted by model distance: nonbonded pdb=" CB LYS A 42 " pdb=" CZ3 TRP A 44 " model vdw 1.225 3.740 nonbonded pdb=" O ALA A 520 " pdb=" OD1 ASN A 521 " model vdw 1.282 3.040 nonbonded pdb=" CB LYS A 42 " pdb=" CH2 TRP A 44 " model vdw 1.306 3.740 nonbonded pdb=" OG SER B 328 " pdb=" CG ARG B 334 " model vdw 1.536 3.440 nonbonded pdb=" OD2 ASP B 330 " pdb=" NH2 ARG B 334 " model vdw 1.788 2.520 ... (remaining 274944 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 'A' and (resid 18 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 43 or (resid 44 and ( \ name N or name CA or name C or name O or name CB )) or resid 45 or (resid 46 and \ (name N or name CA or name C or name O or name CB )) or resid 47 or (resid 48 t \ hrough 49 and (name N or name CA or name C or name O or name CB )) or resid 50 o \ r (resid 52 through 54 and (name N or name CA or name C or name O or name CB )) \ or resid 55 through 59 or (resid 60 and (name N or name CA or name C or name O o \ r name CB )) or resid 61 or (resid 62 through 64 and (name N or name CA or name \ C or name O or name CB )) or resid 65 through 83 or (resid 84 and (name N or nam \ e CA or name C or name O or name CB )) or resid 85 through 87 or (resid 88 throu \ gh 89 and (name N or name CA or name C or name O or name CB )) or resid 90 throu \ gh 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or r \ esid 100 through 103 or (resid 104 and (name N or name CA or name C or name O or \ name CB )) or resid 105 through 109 or (resid 110 through 111 and (name N or na \ me CA or name C or name O or name CB )) or resid 112 through 118 or (resid 119 a \ nd (name N or name CA or name C or name O or name CB )) or resid 120 through 130 \ or (resid 131 and (name N or name CA or name C or name O or name CB )) or resid \ 132 through 180 or (resid 181 through 182 and (name N or name CA or name C or n \ ame O or name CB )) or resid 183 through 189 or (resid 190 and (name N or name C \ A or name C or name O or name CB )) or resid 191 through 192 or (resid 193 throu \ gh 194 and (name N or name CA or name C or name O or name CB )) or resid 195 thr \ ough 199 or (resid 200 through 201 and (name N or name CA or name C or name O or \ name CB )) or resid 202 through 206 or (resid 207 through 208 and (name N or na \ me CA or name C or name O or name CB )) or resid 209 through 220 or (resid 221 a \ nd (name N or name CA or name C or name O or name CB )) or resid 222 through 229 \ or (resid 230 through 231 and (name N or name CA or name C or name O or name CB \ )) or resid 232 through 257 or (resid 258 and (name N or name CA or name C or n \ ame O or name CB )) or resid 259 through 260 or (resid 261 and (name N or name C \ A or name C or name O or name CB )) or resid 262 through 290 or (resid 291 and ( \ name N or name CA or name C or name O or name CB )) or resid 292 through 300 or \ (resid 301 and (name N or name CA or name C or name O or name CB )) or resid 302 \ through 313 or (resid 314 and (name N or name CA or name C or name O or name CB \ )) or resid 315 through 357 or (resid 358 and (name N or name CA or name C or n \ ame O or name CB )) or resid 359 through 362 or (resid 363 and (name N or name C \ A or name C or name O or name CB )) or resid 364 through 365 or (resid 366 throu \ gh 368 and (name N or name CA or name C or name O or name CB )) or resid 369 thr \ ough 422 or (resid 423 and (name N or name CA or name C or name O or name CB )) \ or resid 424 through 441 or (resid 442 and (name N or name CA or name C or name \ O or name CB )) or resid 443 through 447 or (resid 448 and (name N or name CA or \ name C or name O or name CB )) or resid 449 or (resid 450 and (name N or name C \ A or name C or name O or name CB )) or resid 451 through 452 or (resid 453 and ( \ name N or name CA or name C or name O or name CB )) or resid 454 through 467 or \ (resid 468 and (name N or name CA or name C or name O or name CB )) or resid 469 \ through 479 or (resid 480 and (name N or name CA or name C or name O or name CB \ )) or resid 481 through 498 or (resid 499 and (name N or name CA or name C or n \ ame O or name CB )) or resid 500 or (resid 501 through 502 and (name N or name C \ A or name C or name O or name CB )) or resid 503 through 536 or (resid 537 and ( \ name N or name CA or name C or name O or name CB )) or resid 538 through 541 or \ (resid 542 and (name N or name CA or name C or name O or name CB )) or resid 543 \ through 558 or (resid 559 and (name N or name CA or name C or name O or name CB \ )) or resid 560 through 567 or (resid 568 and (name N or name CA or name C or n \ ame O or name CB )) or resid 569 through 570 or (resid 571 and (name N or name C \ A or name C or name O or name CB )) or resid 572 through 573 or (resid 574 and ( \ name N or name CA or name C or name O or name CB )) or resid 575 through 579 or \ (resid 580 and (name N or name CA or name C or name O or name CB )) or resid 581 \ or (resid 582 and (name N or name CA or name C or name O or name CB )) or resid \ 583 through 615 or (resid 616 and (name N or name CA or name C or name O or nam \ e CB )) or resid 618 through 629 or (resid 630 and (name N or name CA or name C \ or name O or name CB )) or resid 631 through 643 or (resid 644 and (name N or na \ me CA or name C or name O or name CB )) or resid 645 through 646 or (resid 647 t \ hrough 648 and (name N or name CA or name C or name O or name CB )) or resid 649 \ through 651 or (resid 652 through 653 and (name N or name CA or name C or name \ O or name CB )) or resid 654 through 662 or (resid 663 and (name N or name CA or \ name C or name O or name CB )) or resid 664 or (resid 665 and (name N or name C \ A or name C or name O or name CB )) or resid 666 through 680 or (resid 681 throu \ gh 682 and (name N or name CA or name C or name O or name CB )) or resid 683 thr \ ough 695 or (resid 696 and (name N or name CA or name C or name O or name CB )) \ or resid 697 or (resid 698 and (name N or name CA or name C or name O or name CB \ )) or resid 710 through 719 or (resid 720 and (name N or name CA or name C or n \ ame O or name CB )) or resid 721 through 725 or resid 732 through 739 or (resid \ 740 and (name N or name CA or name C or name O or name CB )) or resid 741 or res \ id 760 through 763 or (resid 764 through 766 and (name N or name CA or name C or \ name O or name CB )) or resid 767 through 768 or (resid 769 and (name N or name \ CA or name C or name O or name CB )) or resid 770 or (resid 771 through 772 and \ (name N or name CA or name C or name O or name CB )) or resid 773 or (resid 774 \ and (name N or name CA or name C or name O or name CB )) or resid 775 through 7 \ 76 or (resid 777 through 782 and (name N or name CA or name C or name O or name \ CB )) or resid 783 or (resid 784 through 788 and (name N or name CA or name C or \ name O or name CB )) or resid 789 through 790 or (resid 791 through 793 and (na \ me N or name CA or name C or name O or name CB )) or resid 794 through 795 or (r \ esid 796 and (name N or name CA or name C or name O or name CB )) or resid 797 t \ hrough 799 or (resid 800 and (name N or name CA or name C or name O or name CB ) \ ) or resid 801 through 817 or (resid 818 and (name N or name CA or name C or nam \ e O or name CB )) or resid 819 through 861 or (resid 869 through 875 and (name N \ or name CA or name C or name O or name CB )) or resid 876 or (resid 886 through \ 887 and (name N or name CA or name C or name O or name CB )) or resid 888 throu \ gh 889 or (resid 890 through 893 and (name N or name CA or name C or name O or n \ ame CB )) or resid 894 or (resid 895 through 897 and (name N or name CA or name \ C or name O or name CB )) or resid 898 through 901 or (resid 902 and (name N or \ name CA or name C or name O or name CB )) or resid 903 through 909 or (resid 910 \ and (name N or name CA or name C or name O or name CB )) or resid 911 through 9 \ 12 or (resid 913 and (name N or name CA or name C or name O or name CB )) or res \ id 914 through 958 or resid 972 through 982 or (resid 1004 through 1005 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 1006 through 1009 and \ (name N or name CA or name C or name O or name CB )) or resid 1010 through 1011 \ or (resid 1012 and (name N or name CA or name C or name O or name CB )) or resi \ d 1013 or (resid 1014 through 1018 and (name N or name CA or name C or name O or \ name CB )) or resid 1019 or (resid 1020 through 1021 and (name N or name CA or \ name C or name O or name CB )) or resid 1022 through 1030 or (resid 1031 through \ 1032 and (name N or name CA or name C or name O or name CB )) or resid 1033 thr \ ough 1034 or (resid 1035 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1036 through 1104 or (resid 1105 and (name N or name CA or name C or \ name O or name CB )) or resid 1106 or resid 1108 through 1120 or (resid 1122 and \ (name N or name CA or name C or name O or name CB )) or resid 1123 through 1136 \ or (resid 1137 and (name N or name CA or name C or name O or name CB )) or resi \ d 1138 through 1141 or (resid 1144 through 1149 and (name N or name CA or name C \ or name O or name CB )) or resid 1150 or (resid 1151 through 1153 and (name N o \ r name CA or name C or name O or name CB )) or resid 1154 through 1156 or resid \ 1164 through 1168 or (resid 1169 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1170 or (resid 1171 through 1172 and (name N or name CA or na \ me C or name O or name CB )) or resid 1173 or (resid 1174 and (name N or name CA \ or name C or name O or name CB )) or resid 1175 through 1178 or (resid 1179 thr \ ough 1184 and (name N or name CA or name C or name O or name CB )) or resid 1185 \ or (resid 1186 through 1187 and (name N or name CA or name C or name O or name \ CB )) or resid 1188)) selection = (chain 'B' and (resid 18 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 36 or (resid 37 and (name N or nam \ e CA or name C or name O or name CB )) or resid 38 through 39 or (resid 40 and ( \ name N or name CA or name C or name O or name CB )) or resid 41 through 50 or re \ sid 52 through 86 or (resid 87 through 89 and (name N or name CA or name C or na \ me O or name CB )) or resid 90 or (resid 91 through 92 and (name N or name CA or \ name C or name O or name CB )) or resid 93 through 97 or (resid 98 through 99 a \ nd (name N or name CA or name C or name O or name CB )) or resid 100 through 103 \ or (resid 104 and (name N or name CA or name C or name O or name CB )) or resid \ 105 through 109 or (resid 110 through 111 and (name N or name CA or name C or n \ ame O or name CB )) or resid 112 through 142 or (resid 143 and (name N or name C \ A or name C or name O or name CB )) or resid 144 through 146 or (resid 147 throu \ gh 149 and (name N or name CA or name C or name O or name CB )) or resid 150 thr \ ough 154 or (resid 155 through 156 and (name N or name CA or name C or name O or \ name CB )) or resid 157 through 159 or (resid 160 through 161 and (name N or na \ me CA or name C or name O or name CB )) or resid 162 or (resid 163 through 167 a \ nd (name N or name CA or name C or name O or name CB )) or resid 168 or (resid 1 \ 69 and (name N or name CA or name C or name O or name CB )) or resid 170 through \ 180 or (resid 181 through 182 and (name N or name CA or name C or name O or nam \ e CB )) or resid 183 or (resid 184 and (name N or name CA or name C or name O or \ name CB )) or resid 185 through 193 or (resid 194 and (name N or name CA or nam \ e C or name O or name CB )) or resid 195 through 198 or (resid 199 through 201 a \ nd (name N or name CA or name C or name O or name CB )) or resid 202 through 206 \ or (resid 207 through 208 and (name N or name CA or name C or name O or name CB \ )) or resid 209 through 220 or (resid 221 and (name N or name CA or name C or n \ ame O or name CB )) or resid 222 through 229 or (resid 230 through 231 and (name \ N or name CA or name C or name O or name CB )) or resid 232 through 244 or (res \ id 245 and (name N or name CA or name C or name O or name CB )) or resid 246 thr \ ough 268 or (resid 269 through 270 and (name N or name CA or name C or name O or \ name CB )) or resid 271 through 290 or (resid 291 and (name N or name CA or nam \ e C or name O or name CB )) or resid 292 through 294 or (resid 295 through 296 a \ nd (name N or name CA or name C or name O or name CB )) or resid 297 or (resid 2 \ 98 and (name N or name CA or name C or name O or name CB )) or resid 299 through \ 312 or (resid 313 through 314 and (name N or name CA or name C or name O or nam \ e CB )) or resid 315 through 340 or (resid 341 through 345 and (name N or name C \ A or name C or name O or name CB )) or resid 346 through 366 or (resid 367 throu \ gh 368 and (name N or name CA or name C or name O or name CB )) or resid 369 thr \ ough 422 or (resid 423 and (name N or name CA or name C or name O or name CB )) \ or resid 424 through 441 or (resid 442 and (name N or name CA or name C or name \ O or name CB )) or resid 443 through 449 or (resid 450 and (name N or name CA or \ name C or name O or name CB )) or resid 451 through 479 or (resid 480 and (name \ N or name CA or name C or name O or name CB )) or resid 481 through 500 or (res \ id 501 through 502 and (name N or name CA or name C or name O or name CB )) or r \ esid 503 through 558 or (resid 559 and (name N or name CA or name C or name O or \ name CB )) or resid 560 through 567 or (resid 568 and (name N or name CA or nam \ e C or name O or name CB )) or resid 569 through 573 or (resid 574 and (name N o \ r name CA or name C or name O or name CB )) or resid 575 or (resid 576 and (name \ N or name CA or name C or name O or name CB )) or resid 577 through 581 or (res \ id 582 and (name N or name CA or name C or name O or name CB )) or resid 583 thr \ ough 616 or (resid 618 and (name N or name CA or name C or name O or name CB )) \ or resid 619 through 624 or (resid 625 through 626 and (name N or name CA or nam \ e C or name O or name CB )) or resid 627 through 631 or (resid 632 and (name N o \ r name CA or name C or name O or name CB )) or resid 633 through 647 or (resid 6 \ 48 and (name N or name CA or name C or name O or name CB )) or resid 649 through \ 662 or (resid 663 and (name N or name CA or name C or name O or name CB )) or r \ esid 664 through 680 or (resid 681 through 682 and (name N or name CA or name C \ or name O or name CB )) or resid 683 through 685 or (resid 686 and (name N or na \ me CA or name C or name O or name CB )) or resid 687 through 688 or (resid 689 a \ nd (name N or name CA or name C or name O or name CB )) or resid 690 through 693 \ or (resid 694 and (name N or name CA or name C or name O or name CB )) or resid \ 695 or (resid 696 and (name N or name CA or name C or name O or name CB )) or r \ esid 697 or (resid 698 and (name N or name CA or name C or name O or name CB )) \ or resid 710 through 716 or (resid 717 and (name N or name CA or name C or name \ O or name CB )) or resid 718 through 719 or (resid 720 and (name N or name CA or \ name C or name O or name CB )) or resid 721 through 725 or resid 732 through 73 \ 9 or (resid 740 and (name N or name CA or name C or name O or name CB )) or resi \ d 741 or resid 760 through 763 or (resid 764 through 766 and (name N or name CA \ or name C or name O or name CB )) or resid 767 through 768 or (resid 769 and (na \ me N or name CA or name C or name O or name CB )) or resid 770 or (resid 771 thr \ ough 772 and (name N or name CA or name C or name O or name CB )) or resid 773 t \ hrough 780 or (resid 781 through 782 and (name N or name CA or name C or name O \ or name CB )) or resid 783 or (resid 784 through 788 and (name N or name CA or n \ ame C or name O or name CB )) or resid 789 through 790 or (resid 791 through 793 \ and (name N or name CA or name C or name O or name CB )) or resid 794 through 8 \ 06 or (resid 807 and (name N or name CA or name C or name O or name CB )) or res \ id 808 through 852 or (resid 853 through 854 and (name N or name CA or name C or \ name O or name CB )) or resid 855 through 856 or (resid 857 through 858 and (na \ me N or name CA or name C or name O or name CB )) or resid 859 through 869 or (r \ esid 870 through 875 and (name N or name CA or name C or name O or name CB )) or \ resid 876 through 886 or (resid 887 and (name N or name CA or name C or name O \ or name CB )) or resid 888 through 889 or (resid 890 through 893 and (name N or \ name CA or name C or name O or name CB )) or resid 894 or (resid 895 through 897 \ and (name N or name CA or name C or name O or name CB )) or resid 898 through 9 \ 27 or (resid 928 and (name N or name CA or name C or name O or name CB )) or res \ id 929 through 946 or (resid 947 and (name N or name CA or name C or name O or n \ ame CB )) or resid 948 through 958 or (resid 972 through 974 and (name N or name \ CA or name C or name O or name CB )) or resid 975 or (resid 976 through 979 and \ (name N or name CA or name C or name O or name CB )) or resid 980 through 982 o \ r (resid 1004 through 1005 and (name N or name CA or name C or name O or name CB \ )) or resid 1006 through 1013 or (resid 1014 through 1018 and (name N or name C \ A or name C or name O or name CB )) or resid 1019 through 1030 or (resid 1031 th \ rough 1032 and (name N or name CA or name C or name O or name CB )) or resid 103 \ 3 through 1034 or (resid 1035 and (name N or name CA or name C or name O or name \ CB )) or resid 1036 through 1042 or (resid 1043 through 1044 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1045 through 1049 or (resid 1050 \ and (name N or name CA or name C or name O or name CB )) or resid 1051 through \ 1052 or (resid 1053 and (name N or name CA or name C or name O or name CB )) or \ resid 1054 or (resid 1055 through 1059 and (name N or name CA or name C or name \ O or name CB )) or resid 1060 through 1061 or (resid 1062 through 1066 and (name \ N or name CA or name C or name O or name CB )) or resid 1067 or (resid 1068 and \ (name N or name CA or name C or name O or name CB )) or resid 1069 through 1104 \ or (resid 1105 and (name N or name CA or name C or name O or name CB )) or resi \ d 1106 or resid 1108 through 1109 or (resid 1110 and (name N or name CA or name \ C or name O or name CB )) or resid 1111 or (resid 1112 through 1113 and (name N \ or name CA or name C or name O or name CB )) or resid 1114 through 1120 or resid \ 1122 through 1141 or (resid 1144 through 1149 and (name N or name CA or name C \ or name O or name CB )) or resid 1150 or (resid 1151 through 1153 and (name N or \ name CA or name C or name O or name CB )) or resid 1154 through 1168 or (resid \ 1169 and (name N or name CA or name C or name O or name CB )) or (resid 1170 thr \ ough 1172 and (name N or name CA or name C or name O or name CB )) or resid 1173 \ through 1178 or (resid 1179 through 1184 and (name N or name CA or name C or na \ me O or name CB )) or resid 1185 or (resid 1186 through 1187 and (name N or name \ CA or name C or name O or name CB )) or resid 1188)) selection = (chain 'C' and (resid 18 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 43 or (resid 44 and (name N or nam \ e CA or name C or name O or name CB )) or resid 45 or (resid 46 and (name N or n \ ame CA or name C or name O or name CB )) or resid 47 or (resid 48 through 49 and \ (name N or name CA or name C or name O or name CB )) or resid 50 or (resid 52 t \ hrough 54 and (name N or name CA or name C or name O or name CB )) or resid 55 t \ hrough 59 or (resid 60 and (name N or name CA or name C or name O or name CB )) \ or resid 61 or (resid 62 through 64 and (name N or name CA or name C or name O o \ r name CB )) or resid 65 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB )) or resid 85 through 86 or (resid 87 through 89 and (na \ me N or name CA or name C or name O or name CB )) or resid 90 through 98 or (res \ id 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thro \ ugh 118 or (resid 119 and (name N or name CA or name C or name O or name CB )) o \ r resid 120 through 130 or (resid 131 and (name N or name CA or name C or name O \ or name CB )) or resid 132 through 142 or (resid 143 and (name N or name CA or \ name C or name O or name CB )) or resid 144 through 146 or (resid 147 through 14 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 150 through \ 154 or (resid 155 through 156 and (name N or name CA or name C or name O or name \ CB )) or resid 157 through 159 or (resid 160 through 161 and (name N or name CA \ or name C or name O or name CB )) or resid 162 or (resid 163 through 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 183 \ or (resid 184 and (name N or name CA or name C or name O or name CB )) or resid \ 185 through 189 or (resid 190 and (name N or name CA or name C or name O or name \ CB )) or resid 191 through 192 or (resid 193 through 194 and (name N or name CA \ or name C or name O or name CB )) or resid 195 through 198 or (resid 199 throug \ h 201 and (name N or name CA or name C or name O or name CB )) or resid 202 thro \ ugh 230 or (resid 231 and (name N or name CA or name C or name O or name CB )) o \ r resid 232 through 244 or (resid 245 and (name N or name CA or name C or name O \ or name CB )) or resid 246 through 247 or (resid 248 and (name N or name CA or \ name C or name O or name CB )) or resid 249 through 251 or (resid 252 and (name \ N or name CA or name C or name O or name CB )) or resid 253 through 257 or (resi \ d 258 and (name N or name CA or name C or name O or name CB )) or resid 259 thro \ ugh 260 or (resid 261 and (name N or name CA or name C or name O or name CB )) o \ r resid 262 through 268 or (resid 269 through 270 and (name N or name CA or name \ C or name O or name CB )) or resid 271 through 294 or (resid 295 through 296 an \ d (name N or name CA or name C or name O or name CB )) or resid 297 through 312 \ or (resid 313 through 314 and (name N or name CA or name C or name O or name CB \ )) or resid 315 through 340 or (resid 341 through 345 and (name N or name CA or \ name C or name O or name CB )) or resid 346 through 357 or (resid 358 and (name \ N or name CA or name C or name O or name CB )) or resid 359 through 362 or (resi \ d 363 and (name N or name CA or name C or name O or name CB )) or resid 364 thro \ ugh 366 or (resid 367 through 368 and (name N or name CA or name C or name O or \ name CB )) or resid 369 through 409 or (resid 410 and (name N or name CA or name \ C or name O or name CB )) or resid 411 through 447 or (resid 448 and (name N or \ name CA or name C or name O or name CB )) or resid 449 through 452 or (resid 45 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 454 through \ 467 or (resid 468 and (name N or name CA or name C or name O or name CB )) or re \ sid 469 through 498 or (resid 499 and (name N or name CA or name C or name O or \ name CB )) or resid 500 through 501 or (resid 502 and (name N or name CA or name \ C or name O or name CB )) or resid 503 through 536 or (resid 537 and (name N or \ name CA or name C or name O or name CB )) or resid 538 through 541 or (resid 54 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 543 through \ 570 or (resid 571 and (name N or name CA or name C or name O or name CB )) or re \ sid 572 through 575 or (resid 576 and (name N or name CA or name C or name O or \ name CB )) or resid 577 through 579 or (resid 580 and (name N or name CA or name \ C or name O or name CB )) or resid 581 through 586 or (resid 587 and (name N or \ name CA or name C or name O or name CB )) or resid 588 through 615 or (resid 61 \ 6 through 618 and (name N or name CA or name C or name O or name CB )) or resid \ 619 through 624 or (resid 625 through 626 and (name N or name CA or name C or na \ me O or name CB )) or resid 627 through 629 or (resid 630 and (name N or name CA \ or name C or name O or name CB )) or resid 631 or (resid 632 and (name N or nam \ e CA or name C or name O or name CB )) or resid 633 through 637 or (resid 638 an \ d (name N or name CA or name C or name O or name CB )) or resid 639 through 643 \ or (resid 644 and (name N or name CA or name C or name O or name CB )) or resid \ 645 through 646 or (resid 647 through 648 and (name N or name CA or name C or na \ me O or name CB )) or resid 649 through 651 or (resid 652 through 653 and (name \ N or name CA or name C or name O or name CB )) or resid 654 through 681 or (resi \ d 682 and (name N or name CA or name C or name O or name CB )) or resid 683 thro \ ugh 685 or (resid 686 and (name N or name CA or name C or name O or name CB )) o \ r resid 687 through 688 or (resid 689 and (name N or name CA or name C or name O \ or name CB )) or resid 690 through 725 or resid 732 through 741 or resid 760 th \ rough 773 or (resid 774 and (name N or name CA or name C or name O or name CB )) \ or resid 775 through 791 or (resid 792 through 793 and (name N or name CA or na \ me C or name O or name CB )) or resid 794 through 795 or (resid 796 and (name N \ or name CA or name C or name O or name CB )) or resid 797 through 799 or (resid \ 800 and (name N or name CA or name C or name O or name CB )) or resid 801 throug \ h 806 or (resid 807 and (name N or name CA or name C or name O or name CB )) or \ resid 808 through 817 or (resid 818 and (name N or name CA or name C or name O o \ r name CB )) or resid 819 through 852 or (resid 853 through 854 and (name N or n \ ame CA or name C or name O or name CB )) or resid 855 through 856 or (resid 857 \ through 858 and (name N or name CA or name C or name O or name CB )) or resid 85 \ 9 through 861 or resid 869 through 876 or resid 886 through 896 or (resid 897 an \ d (name N or name CA or name C or name O or name CB )) or resid 898 through 901 \ or (resid 902 and (name N or name CA or name C or name O or name CB )) or resid \ 903 through 909 or (resid 910 and (name N or name CA or name C or name O or name \ CB )) or resid 911 through 912 or (resid 913 and (name N or name CA or name C o \ r name O or name CB )) or resid 914 through 927 or (resid 928 and (name N or nam \ e CA or name C or name O or name CB )) or resid 929 through 946 or (resid 947 an \ d (name N or name CA or name C or name O or name CB )) or resid 948 through 958 \ or (resid 972 through 974 and (name N or name CA or name C or name O or name CB \ )) or resid 975 or (resid 976 through 979 and (name N or name CA or name C or na \ me O or name CB )) or resid 980 through 1007 or (resid 1008 through 1009 and (na \ me N or name CA or name C or name O or name CB )) or resid 1010 through 1011 or \ (resid 1012 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 13 through 1019 or (resid 1020 through 1021 and (name N or name CA or name C or \ name O or name CB )) or resid 1022 through 1042 or (resid 1043 through 1044 and \ (name N or name CA or name C or name O or name CB )) or resid 1045 through 1049 \ or (resid 1050 and (name N or name CA or name C or name O or name CB )) or resid \ 1051 through 1052 or (resid 1053 and (name N or name CA or name C or name O or \ name CB )) or resid 1054 or (resid 1055 through 1059 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1060 through 1061 or (resid 1062 through \ 1066 and (name N or name CA or name C or name O or name CB )) or resid 1067 or ( \ resid 1068 and (name N or name CA or name C or name O or name CB )) or resid 106 \ 9 through 1120 or (resid 1122 and (name N or name CA or name C or name O or name \ CB )) or resid 1123 through 1136 or (resid 1137 and (name N or name CA or name \ C or name O or name CB )) or resid 1138 through 1148 or (resid 1149 and (name N \ or name CA or name C or name O or name CB )) or resid 1150 through 1156 or resid \ 1164 through 1188)) } ncs_group { reference = (chain 'D' and (resid 4 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 122 or (resid 123 and (name N or na \ me CA or name C or name O or name CB )) or resid 124 through 137 or (resid 138 a \ nd (name N or name CA or name C or name O or name CB )) or resid 139 through 151 \ or (resid 152 and (name N or name CA or name C or name O or name CB )) or resid \ 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) or r \ esid 155 through 175 or (resid 176 through 177 and (name N or name CA or name C \ or name O or name CB )) or resid 178 through 199 or (resid 200 and (name N or na \ me CA or name C or name O or name CB )) or resid 201 through 219)) selection = (chain 'F' and (resid 4 through 73 or (resid 74 and (name N or name CA or name C \ or name O or name CB )) or resid 75 through 127 or (resid 128 through 129 and ( \ name N or name CA or name C or name O or name CB )) or resid 130 through 142 or \ (resid 143 and (name N or name CA or name C or name O or name CB )) or resid 144 \ through 151 or (resid 152 and (name N or name CA or name C or name O or name CB \ )) or resid 153 or (resid 154 and (name N or name CA or name C or name O or nam \ e CB )) or resid 155 through 174 or (resid 175 through 177 and (name N or name C \ A or name C or name O or name CB )) or resid 178 through 199 or (resid 200 and ( \ name N or name CA or name C or name O or name CB )) or resid 201 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 219 \ )) selection = (chain 'H' and (resid 4 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 127 or (resid 128 through 129 and ( \ name N or name CA or name C or name O or name CB )) or resid 130 through 142 or \ (resid 143 and (name N or name CA or name C or name O or name CB )) or resid 144 \ through 174 or (resid 175 through 177 and (name N or name CA or name C or name \ O or name CB )) or resid 178 through 217 or (resid 218 and (name N or name CA or \ name C or name O or name CB )) or resid 219)) } ncs_group { reference = (chain 'E' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 56 or (resid 57 through 61 and (nam \ e N or name CA or name C or name O or name CB )) or resid 62 through 78 or (resi \ d 79 and (name N or name CA or name C or name O or name CB )) or resid 80 throug \ h 102 or (resid 103 through 104 and (name N or name CA or name C or name O or na \ me CB )) or resid 105 through 106 or (resid 107 and (name N or name CA or name C \ or name O or name CB )) or resid 108 through 109 or (resid 110 and (name N or n \ ame CA or name C or name O or name CB )) or resid 111 through 160 or (resid 161 \ through 162 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 3 through 165 or (resid 166 and (name N or name CA or name C or name O or name C \ B )) or resid 167 through 227)) selection = (chain 'G' and (resid 1 through 28 or (resid 29 through 30 and (name N or name C \ A or name C or name O or name CB )) or resid 31 through 51 or (resid 52 through \ 54 and (name N or name CA or name C or name O or name CB )) or resid 55 through \ 56 or (resid 57 through 61 and (name N or name CA or name C or name O or name CB \ )) or resid 62 through 97 or (resid 98 and (name N or name CA or name C or name \ O or name CB )) or resid 99 through 102 or (resid 103 through 104 and (name N o \ r name CA or name C or name O or name CB )) or resid 105 through 106 or (resid 1 \ 07 and (name N or name CA or name C or name O or name CB )) or resid 108 through \ 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) or r \ esid 111 through 115 or (resid 116 and (name N or name CA or name C or name O or \ name CB )) or resid 117 through 132 or (resid 133 and (name N or name CA or nam \ e C or name O or name CB )) or resid 134 through 137 or (resid 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 160 or (resid 1 \ 61 through 162 and (name N or name CA or name C or name O or name CB )) or resid \ 163 through 165 or (resid 166 and (name N or name CA or name C or name O or nam \ e CB )) or resid 167 through 227)) selection = (chain 'I' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 78 or (resid 79 and (nam \ e N or name CA or name C or name O or name CB )) or resid 80 through 97 or (resi \ d 98 and (name N or name CA or name C or name O or name CB )) or resid 99 throug \ h 115 or (resid 116 and (name N or name CA or name C or name O or name CB )) or \ resid 117 through 132 or (resid 133 and (name N or name CA or name C or name O o \ r name CB )) or resid 134 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 142 or (resid 143 and (name N \ or name CA or name C or name O or name CB )) or resid 144 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throug \ h 227)) } 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: 2.030 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: 0.030 Extract box with map and model: 1.610 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 98.580 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.190 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: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4839 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 : 0.013 0.064 35159 Z= 0.883 Angle : 1.540 14.320 47932 Z= 1.183 Chirality : 0.106 0.576 5550 Planarity : 0.004 0.071 6205 Dihedral : 13.593 82.266 12134 Min Nonbonded Distance : 1.225 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 1.13 % Allowed : 3.97 % Favored : 94.90 % Rotamer: Outliers : 8.11 % Allowed : 10.19 % Favored : 81.71 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.46 (0.12), residues: 4595 helix: 4.29 (0.18), residues: 721 sheet: 1.94 (0.15), residues: 1174 loop : -0.46 (0.11), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 120 HIS 0.006 0.001 HIS C1122 PHE 0.017 0.002 PHE A1116 TYR 0.031 0.002 TYR A 314 ARG 0.005 0.001 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 502 time to evaluate : 3.662 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: A 323 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.6628 (t80) REVERT: A 424 THR cc_start: 0.2110 (OUTLIER) cc_final: 0.1895 (p) REVERT: A 795 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.6913 (mm) REVERT: A 799 ILE cc_start: 0.7978 (pt) cc_final: 0.7516 (pt) REVERT: A 903 PRO cc_start: 0.0716 (Cg_endo) cc_final: 0.0382 (Cg_exo) REVERT: A 1127 VAL cc_start: 0.7551 (t) cc_final: 0.7337 (m) REVERT: A 1149 VAL cc_start: 0.4306 (OUTLIER) cc_final: 0.4100 (t) REVERT: B 400 LYS cc_start: 0.7169 (tptm) cc_final: 0.6837 (ttpt) REVERT: B 433 ILE cc_start: 0.5518 (OUTLIER) cc_final: 0.4273 (pt) REVERT: B 477 THR cc_start: 0.0238 (OUTLIER) cc_final: -0.0063 (p) REVERT: B 620 CYS cc_start: 0.3455 (OUTLIER) cc_final: 0.2895 (m) REVERT: B 667 THR cc_start: 0.6428 (p) cc_final: 0.6227 (p) REVERT: B 696 MET cc_start: 0.6594 (ppp) cc_final: 0.6120 (ptm) REVERT: B 970 ILE cc_start: 0.4782 (OUTLIER) cc_final: 0.4581 (tt) REVERT: B 983 VAL cc_start: 0.5647 (OUTLIER) cc_final: 0.4192 (m) REVERT: B 989 VAL cc_start: 0.6814 (OUTLIER) cc_final: 0.6194 (p) REVERT: C 393 PRO cc_start: 0.4528 (Cg_exo) cc_final: 0.4298 (Cg_endo) REVERT: C 395 GLN cc_start: 0.4649 (mm-40) cc_final: 0.4378 (mm-40) REVERT: C 401 ARG cc_start: 0.2987 (OUTLIER) cc_final: 0.2419 (ptp-110) REVERT: C 473 PHE cc_start: 0.4220 (p90) cc_final: 0.3980 (p90) REVERT: C 523 TYR cc_start: 0.3815 (m-80) cc_final: 0.3284 (m-10) REVERT: C 606 TYR cc_start: 0.5467 (OUTLIER) cc_final: 0.4901 (p90) REVERT: C 639 VAL cc_start: 0.3151 (OUTLIER) cc_final: 0.2707 (t) REVERT: C 651 LEU cc_start: 0.6874 (mt) cc_final: 0.6195 (mt) REVERT: C 938 LEU cc_start: 0.4710 (OUTLIER) cc_final: 0.4484 (tp) REVERT: C 1040 LEU cc_start: 0.5791 (OUTLIER) cc_final: 0.5477 (mt) REVERT: C 1086 LEU cc_start: 0.8235 (mt) cc_final: 0.7962 (tp) REVERT: D 52 TYR cc_start: 0.3886 (t80) cc_final: 0.2289 (t80) REVERT: D 181 SER cc_start: -0.0051 (OUTLIER) cc_final: -0.0260 (t) REVERT: D 186 LEU cc_start: 0.0456 (OUTLIER) cc_final: -0.0047 (tp) REVERT: E 68 PHE cc_start: 0.3515 (m-10) cc_final: 0.3091 (m-80) REVERT: E 83 MET cc_start: 0.4544 (mtm) cc_final: 0.4152 (mpp) REVERT: E 186 LEU cc_start: 0.3263 (OUTLIER) cc_final: 0.2974 (mm) REVERT: F 6 GLN cc_start: 0.5327 (OUTLIER) cc_final: 0.4991 (mp10) REVERT: F 7 MET cc_start: 0.4020 (tmm) cc_final: 0.3324 (tmm) REVERT: F 36 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5061 (mm) REVERT: F 75 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7358 (m) REVERT: F 122 ILE cc_start: 0.1688 (tp) cc_final: 0.1467 (tp) REVERT: G 83 MET cc_start: 0.4753 (mtm) cc_final: 0.4309 (mpp) REVERT: G 166 VAL cc_start: -0.1241 (OUTLIER) cc_final: -0.1559 (p) REVERT: G 168 VAL cc_start: 0.1191 (OUTLIER) cc_final: 0.0502 (p) REVERT: G 191 LEU cc_start: 0.2287 (OUTLIER) cc_final: 0.1972 (mp) REVERT: H 51 ILE cc_start: 0.4068 (OUTLIER) cc_final: 0.3397 (tt) REVERT: H 86 PHE cc_start: 0.4766 (m-10) cc_final: 0.4553 (m-10) REVERT: H 112 LYS cc_start: 0.5651 (mtmm) cc_final: 0.5425 (mttp) REVERT: I 48 VAL cc_start: 0.6598 (OUTLIER) cc_final: 0.6360 (p) REVERT: I 93 VAL cc_start: 0.4254 (OUTLIER) cc_final: 0.3995 (p) REVERT: I 95 TYR cc_start: 0.5023 (m-80) cc_final: 0.4435 (m-80) REVERT: I 194 LEU cc_start: -0.0297 (OUTLIER) cc_final: -0.0506 (pp) outliers start: 296 outliers final: 53 residues processed: 750 average time/residue: 0.4371 time to fit residues: 542.0144 Evaluate side-chains 333 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 252 time to evaluate : 3.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 606 TYR Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 161 TYR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 200 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 389 optimal weight: 0.0370 chunk 349 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 361 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 219 optimal weight: 8.9990 chunk 268 optimal weight: 5.9990 chunk 418 optimal weight: 0.0870 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN A 516 GLN A 522 GLN A 627 GLN A 733 GLN A 765 ASN A 785 ASN ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 ASN A 999 ASN A1020 GLN A1084 GLN A1146 HIS A1163 ASN B 114 ASN B 319 GLN B 346 GLN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 ASN B 833 GLN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 GLN ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1079 ASN B1110 GLN B1129 ASN C 72 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 277 ASN C 280 GLN ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 GLN C 618 GLN C 733 GLN C 832 ASN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 GLN C1027 ASN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1129 ASN ** C1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1176 ASN C1177 ASN D 160 GLN D 171 GLN E 31 ASN E 35 HIS ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN G 122 GLN G 187 GLN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN H 129 GLN H 160 GLN H 171 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5037 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35159 Z= 0.210 Angle : 0.670 10.671 47932 Z= 0.356 Chirality : 0.044 0.226 5550 Planarity : 0.004 0.053 6205 Dihedral : 6.657 57.600 5107 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.44 % Allowed : 3.29 % Favored : 96.27 % Rotamer: Outliers : 4.24 % Allowed : 14.70 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.69 (0.12), residues: 4595 helix: 2.53 (0.18), residues: 769 sheet: 1.65 (0.15), residues: 1171 loop : -0.78 (0.11), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 44 HIS 0.008 0.001 HIS B 81 PHE 0.025 0.002 PHE B 266 TYR 0.048 0.002 TYR A 909 ARG 0.007 0.001 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 268 time to evaluate : 3.554 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: A 420 VAL cc_start: 0.2622 (OUTLIER) cc_final: 0.2324 (m) REVERT: A 795 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7766 (mt) REVERT: A 1127 VAL cc_start: 0.8177 (t) cc_final: 0.7957 (m) REVERT: A 1149 VAL cc_start: 0.4646 (OUTLIER) cc_final: 0.4199 (t) REVERT: B 477 THR cc_start: 0.0176 (OUTLIER) cc_final: -0.0084 (p) REVERT: B 565 GLU cc_start: 0.5756 (OUTLIER) cc_final: 0.4964 (pm20) REVERT: B 620 CYS cc_start: 0.3660 (OUTLIER) cc_final: 0.2914 (m) REVERT: B 667 THR cc_start: 0.6297 (p) cc_final: 0.6055 (p) REVERT: B 696 MET cc_start: 0.6445 (ppp) cc_final: 0.5929 (ptm) REVERT: C 58 TYR cc_start: 0.6174 (t80) cc_final: 0.5629 (t80) REVERT: C 171 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7310 (pt) REVERT: C 393 PRO cc_start: 0.4512 (Cg_exo) cc_final: 0.3736 (Cg_endo) REVERT: C 397 TYR cc_start: 0.3326 (p90) cc_final: 0.2753 (p90) REVERT: C 609 TYR cc_start: 0.3349 (OUTLIER) cc_final: 0.2898 (m-80) REVERT: C 906 MET cc_start: 0.0918 (mmp) cc_final: 0.0549 (mmp) REVERT: D 52 TYR cc_start: 0.4394 (t80) cc_final: 0.2726 (t80) REVERT: E 68 PHE cc_start: 0.3410 (m-10) cc_final: 0.3049 (m-80) REVERT: E 83 MET cc_start: 0.4356 (mtm) cc_final: 0.3362 (mpp) REVERT: E 207 THR cc_start: 0.3920 (OUTLIER) cc_final: 0.3452 (m) REVERT: F 6 GLN cc_start: 0.5032 (OUTLIER) cc_final: 0.4536 (mp10) REVERT: F 36 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.5995 (mm) REVERT: F 92 GLN cc_start: 0.2408 (OUTLIER) cc_final: 0.1599 (mp10) REVERT: G 83 MET cc_start: 0.5035 (mtm) cc_final: 0.3976 (mpp) REVERT: G 166 VAL cc_start: 0.0041 (OUTLIER) cc_final: -0.0543 (p) REVERT: I 6 GLU cc_start: 0.1809 (OUTLIER) cc_final: 0.1498 (mm-30) REVERT: I 48 VAL cc_start: 0.6992 (OUTLIER) cc_final: 0.6757 (p) REVERT: I 68 PHE cc_start: 0.3050 (m-80) cc_final: 0.2803 (m-80) REVERT: I 83 MET cc_start: 0.5524 (mtm) cc_final: 0.5288 (mtt) REVERT: I 95 TYR cc_start: 0.4868 (m-80) cc_final: 0.4523 (m-80) REVERT: I 194 LEU cc_start: -0.0004 (OUTLIER) cc_final: -0.0220 (pp) outliers start: 155 outliers final: 79 residues processed: 404 average time/residue: 0.4134 time to fit residues: 281.7434 Evaluate side-chains 287 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 192 time to evaluate : 3.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 934 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1156 CYS Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 92 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 161 TYR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 194 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 232 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 348 optimal weight: 20.0000 chunk 285 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 419 optimal weight: 4.9990 chunk 453 optimal weight: 30.0000 chunk 373 optimal weight: 4.9990 chunk 415 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 336 optimal weight: 9.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 114 ASN A 218 ASN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN A 733 GLN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN A1084 GLN A1163 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN B 688 GLN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 ASN ** B1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 ASN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 HIS ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 815 GLN C 839 ASN C1023 GLN ** C1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1177 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN D 171 GLN ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 GLN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN I 35 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5600 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.195 35159 Z= 0.582 Angle : 1.098 14.882 47932 Z= 0.593 Chirality : 0.060 0.504 5550 Planarity : 0.009 0.121 6205 Dihedral : 8.632 59.696 5046 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 30.07 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.91 % Favored : 92.61 % Rotamer: Outliers : 6.11 % Allowed : 14.81 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.38 (0.12), residues: 4595 helix: -0.42 (0.17), residues: 778 sheet: 0.38 (0.15), residues: 1152 loop : -1.74 (0.11), residues: 2665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.004 TRP C 553 HIS 0.016 0.004 HIS C 836 PHE 0.047 0.005 PHE B 112 TYR 0.063 0.005 TYR B 274 ARG 0.021 0.002 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 235 time to evaluate : 3.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7685 (mmm) REVERT: A 323 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7345 (t80) REVERT: A 389 LEU cc_start: 0.4460 (OUTLIER) cc_final: 0.3674 (tp) REVERT: A 397 TYR cc_start: 0.3544 (p90) cc_final: 0.2747 (p90) REVERT: A 448 TYR cc_start: 0.2004 (t80) cc_final: 0.1738 (t80) REVERT: A 523 TYR cc_start: 0.4452 (m-80) cc_final: 0.3866 (m-10) REVERT: A 549 GLU cc_start: 0.3808 (OUTLIER) cc_final: 0.3267 (tp30) REVERT: A 985 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.6936 (mm) REVERT: A 1000 LYS cc_start: 0.3988 (OUTLIER) cc_final: 0.3367 (tmmt) REVERT: A 1104 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8340 (m-40) REVERT: A 1116 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.6184 (p90) REVERT: A 1169 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7411 (m-40) REVERT: A 1184 TRP cc_start: 0.2168 (OUTLIER) cc_final: 0.1682 (t-100) REVERT: B 161 MET cc_start: 0.3633 (tpp) cc_final: 0.3366 (ttm) REVERT: B 240 MET cc_start: 0.4942 (mpp) cc_final: 0.4677 (mpp) REVERT: B 433 ILE cc_start: 0.6064 (OUTLIER) cc_final: 0.5439 (pt) REVERT: B 438 TYR cc_start: 0.4760 (OUTLIER) cc_final: 0.4170 (m-80) REVERT: B 477 THR cc_start: -0.1146 (OUTLIER) cc_final: -0.1523 (p) REVERT: B 505 ARG cc_start: 0.3837 (tmt170) cc_final: 0.2847 (ttp-110) REVERT: B 569 MET cc_start: 0.0659 (tpp) cc_final: 0.0455 (tpp) REVERT: B 620 CYS cc_start: 0.3145 (OUTLIER) cc_final: 0.2711 (m) REVERT: B 662 ILE cc_start: 0.6561 (OUTLIER) cc_final: 0.6240 (tp) REVERT: C 131 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.7172 (mt) REVERT: C 636 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6436 (pm20) REVERT: C 1123 ILE cc_start: 0.6275 (mt) cc_final: 0.5918 (mt) REVERT: E 32 TYR cc_start: 0.5887 (OUTLIER) cc_final: 0.4803 (m-80) REVERT: E 207 THR cc_start: 0.3169 (OUTLIER) cc_final: 0.2457 (m) REVERT: F 7 MET cc_start: 0.4213 (tmm) cc_final: 0.3802 (tmm) REVERT: G 19 ARG cc_start: 0.4684 (tpm170) cc_final: 0.3666 (tpp80) REVERT: G 36 TRP cc_start: -0.0173 (m100) cc_final: -0.1009 (m100) REVERT: G 83 MET cc_start: 0.5129 (mtm) cc_final: 0.4262 (mpp) REVERT: G 122 GLN cc_start: 0.5583 (mm-40) cc_final: 0.5029 (tp-100) REVERT: G 124 THR cc_start: 0.0415 (OUTLIER) cc_final: 0.0183 (t) REVERT: H 51 ILE cc_start: 0.5268 (OUTLIER) cc_final: 0.4985 (tt) REVERT: I 6 GLU cc_start: 0.2039 (OUTLIER) cc_final: 0.1112 (mm-30) REVERT: I 34 MET cc_start: 0.4160 (tpp) cc_final: 0.3945 (mpp) REVERT: I 68 PHE cc_start: 0.3771 (m-80) cc_final: 0.3318 (m-80) REVERT: I 80 TYR cc_start: 0.6824 (m-10) cc_final: 0.6490 (m-10) REVERT: I 87 ARG cc_start: 0.6288 (mtm110) cc_final: 0.5925 (mtm110) REVERT: I 95 TYR cc_start: 0.4938 (m-80) cc_final: 0.4614 (m-80) outliers start: 223 outliers final: 116 residues processed: 440 average time/residue: 0.4383 time to fit residues: 321.8523 Evaluate side-chains 325 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 187 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 824 TYR Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 ASN Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1169 ASN Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1184 TRP Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 636 GLN Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 809 TYR Chi-restraints excluded: chain C residue 934 VAL Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1089 SER Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain C residue 1156 CYS Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 194 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 414 optimal weight: 6.9990 chunk 315 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 46 optimal weight: 0.0030 chunk 200 optimal weight: 0.0570 chunk 281 optimal weight: 8.9990 chunk 420 optimal weight: 20.0000 chunk 445 optimal weight: 0.0470 chunk 219 optimal weight: 7.9990 chunk 398 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.6210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 785 ASN A 848 ASN B 104 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN B 733 GLN B 765 ASN B 819 GLN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 ASN C 277 ASN C 280 GLN C 319 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 GLN C1042 ASN ** C1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 93 GLN ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN F 142 ASN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 ASN H 143 ASN H 160 GLN H 171 GLN ** H 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5453 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35159 Z= 0.190 Angle : 0.660 10.093 47932 Z= 0.349 Chirality : 0.044 0.258 5550 Planarity : 0.004 0.081 6205 Dihedral : 6.434 59.231 5018 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.86 % Favored : 94.88 % Rotamer: Outliers : 3.07 % Allowed : 18.10 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.80 (0.12), residues: 4595 helix: 0.93 (0.18), residues: 764 sheet: 0.56 (0.15), residues: 1138 loop : -1.53 (0.11), residues: 2693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 253 HIS 0.007 0.001 HIS E 35 PHE 0.041 0.002 PHE C1044 TYR 0.047 0.002 TYR A 397 ARG 0.007 0.001 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 220 time to evaluate : 3.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.6633 (t80) REVERT: A 523 TYR cc_start: 0.4288 (m-80) cc_final: 0.3652 (m-10) REVERT: A 1012 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.7002 (t80) REVERT: A 1169 ASN cc_start: 0.7615 (OUTLIER) cc_final: 0.7373 (m-40) REVERT: A 1184 TRP cc_start: 0.1853 (OUTLIER) cc_final: 0.1516 (t-100) REVERT: B 240 MET cc_start: 0.5128 (mpp) cc_final: 0.4842 (mpp) REVERT: B 477 THR cc_start: -0.1300 (OUTLIER) cc_final: -0.1647 (p) REVERT: B 505 ARG cc_start: 0.3564 (tmt170) cc_final: 0.2890 (ttp-170) REVERT: B 620 CYS cc_start: 0.2697 (OUTLIER) cc_final: 0.2387 (m) REVERT: B 967 PHE cc_start: 0.3683 (m-10) cc_final: 0.3306 (m-80) REVERT: C 438 TYR cc_start: 0.2551 (OUTLIER) cc_final: 0.2308 (m-80) REVERT: D 20 ASP cc_start: 0.6742 (t0) cc_final: 0.6516 (m-30) REVERT: D 52 TYR cc_start: 0.4707 (t80) cc_final: 0.2856 (t80) REVERT: E 151 THR cc_start: 0.2882 (OUTLIER) cc_final: 0.2388 (m) REVERT: E 207 THR cc_start: 0.3625 (OUTLIER) cc_final: 0.2983 (m) REVERT: F 7 MET cc_start: 0.3903 (tmm) cc_final: 0.3648 (tmm) REVERT: G 36 TRP cc_start: -0.0303 (m100) cc_final: -0.0785 (m100) REVERT: G 83 MET cc_start: 0.4900 (mtm) cc_final: 0.4199 (mpp) REVERT: H 7 MET cc_start: 0.4738 (tmm) cc_final: 0.4420 (tmm) REVERT: I 6 GLU cc_start: 0.1674 (OUTLIER) cc_final: 0.1149 (mm-30) REVERT: I 76 LYS cc_start: 0.6777 (ttpt) cc_final: 0.6270 (ttpt) REVERT: I 192 TYR cc_start: 0.5381 (m-80) cc_final: 0.5123 (m-80) outliers start: 112 outliers final: 63 residues processed: 321 average time/residue: 0.4493 time to fit residues: 240.4630 Evaluate side-chains 268 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 195 time to evaluate : 3.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1169 ASN Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1184 TRP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 452 MET Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1055 ILE Chi-restraints excluded: chain C residue 1059 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1089 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 64 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 371 optimal weight: 20.0000 chunk 252 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 331 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 380 optimal weight: 0.0370 chunk 308 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 227 optimal weight: 5.9990 chunk 399 optimal weight: 20.0000 chunk 112 optimal weight: 0.0010 overall best weight: 3.0070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 HIS A1009 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN C1042 ASN ** C1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN ** H 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5558 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 35159 Z= 0.270 Angle : 0.698 9.230 47932 Z= 0.370 Chirality : 0.045 0.284 5550 Planarity : 0.005 0.049 6205 Dihedral : 6.422 59.613 5015 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.38 % Favored : 93.38 % Rotamer: Outliers : 4.00 % Allowed : 17.88 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.03 (0.12), residues: 4595 helix: 0.81 (0.19), residues: 755 sheet: 0.22 (0.15), residues: 1211 loop : -1.66 (0.11), residues: 2629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 553 HIS 0.007 0.001 HIS A1138 PHE 0.049 0.003 PHE C1044 TYR 0.038 0.002 TYR B 105 ARG 0.014 0.001 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 199 time to evaluate : 4.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7075 (t80) REVERT: A 523 TYR cc_start: 0.4065 (m-80) cc_final: 0.3558 (m-10) REVERT: A 549 GLU cc_start: 0.4264 (OUTLIER) cc_final: 0.3644 (tp30) REVERT: A 1104 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8386 (t0) REVERT: A 1116 PHE cc_start: 0.6463 (OUTLIER) cc_final: 0.5759 (p90) REVERT: A 1184 TRP cc_start: 0.1897 (OUTLIER) cc_final: 0.1571 (t-100) REVERT: B 240 MET cc_start: 0.5371 (mpp) cc_final: 0.5043 (mpp) REVERT: B 477 THR cc_start: -0.1615 (OUTLIER) cc_final: -0.1844 (p) REVERT: B 505 ARG cc_start: 0.3858 (tmt170) cc_final: 0.3073 (ttp-110) REVERT: B 620 CYS cc_start: 0.2806 (OUTLIER) cc_final: 0.2444 (m) REVERT: B 662 ILE cc_start: 0.6614 (OUTLIER) cc_final: 0.6290 (tp) REVERT: C 438 TYR cc_start: 0.2891 (OUTLIER) cc_final: 0.2637 (m-80) REVERT: E 151 THR cc_start: 0.2735 (OUTLIER) cc_final: 0.2511 (m) REVERT: E 207 THR cc_start: 0.3362 (OUTLIER) cc_final: 0.2672 (m) REVERT: F 74 PHE cc_start: 0.4746 (m-80) cc_final: 0.4455 (m-80) REVERT: G 19 ARG cc_start: 0.4595 (tpp-160) cc_final: 0.4303 (tpp-160) REVERT: G 83 MET cc_start: 0.4992 (mtm) cc_final: 0.4189 (mpp) REVERT: G 194 LEU cc_start: 0.0394 (mt) cc_final: 0.0178 (mt) REVERT: H 29 SER cc_start: 0.2044 (OUTLIER) cc_final: 0.1549 (p) REVERT: I 6 GLU cc_start: 0.1885 (OUTLIER) cc_final: 0.1511 (mm-30) REVERT: I 32 TYR cc_start: 0.6702 (m-80) cc_final: 0.6445 (m-80) REVERT: I 122 GLN cc_start: 0.4465 (tp40) cc_final: 0.3790 (tp40) REVERT: I 192 TYR cc_start: 0.5510 (m-80) cc_final: 0.5245 (m-80) outliers start: 146 outliers final: 102 residues processed: 329 average time/residue: 0.4161 time to fit residues: 231.7305 Evaluate side-chains 291 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 176 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1104 ASN Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1184 TRP Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 797 THR Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 1059 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1089 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 138 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 149 optimal weight: 2.9990 chunk 401 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 446 optimal weight: 10.0000 chunk 370 optimal weight: 30.0000 chunk 206 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 147 optimal weight: 9.9990 chunk 234 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN A 421 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 ASN ** C 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 82 GLN ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 GLN H 171 GLN ** H 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5571 moved from start: 0.6487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35159 Z= 0.228 Angle : 0.653 9.672 47932 Z= 0.346 Chirality : 0.044 0.176 5550 Planarity : 0.004 0.051 6205 Dihedral : 6.209 58.616 5015 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.41 % Favored : 93.33 % Rotamer: Outliers : 3.83 % Allowed : 18.81 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.08 (0.12), residues: 4595 helix: 0.89 (0.19), residues: 761 sheet: 0.14 (0.15), residues: 1222 loop : -1.71 (0.11), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 553 HIS 0.006 0.001 HIS A1138 PHE 0.026 0.002 PHE A 239 TYR 0.027 0.002 TYR B 105 ARG 0.011 0.001 ARG B1179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 196 time to evaluate : 3.994 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: A 385 PHE cc_start: 0.3643 (m-80) cc_final: 0.3209 (m-80) REVERT: A 523 TYR cc_start: 0.4209 (m-80) cc_final: 0.3681 (m-10) REVERT: A 549 GLU cc_start: 0.4130 (OUTLIER) cc_final: 0.3489 (tp30) REVERT: A 795 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8204 (mm) REVERT: A 1012 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.7015 (t80) REVERT: A 1184 TRP cc_start: 0.1719 (OUTLIER) cc_final: 0.1358 (t-100) REVERT: B 240 MET cc_start: 0.5881 (mpp) cc_final: 0.5512 (mpp) REVERT: B 505 ARG cc_start: 0.3774 (tmt170) cc_final: 0.3110 (ttp-110) REVERT: B 620 CYS cc_start: 0.3045 (OUTLIER) cc_final: 0.2788 (m) REVERT: B 662 ILE cc_start: 0.6596 (OUTLIER) cc_final: 0.6320 (tp) REVERT: B 757 MET cc_start: 0.2475 (tpp) cc_final: 0.2257 (mmm) REVERT: C 240 MET cc_start: 0.6378 (mmm) cc_final: 0.5972 (mmm) REVERT: C 438 TYR cc_start: 0.3202 (OUTLIER) cc_final: 0.2901 (m-80) REVERT: D 52 TYR cc_start: 0.4960 (t80) cc_final: 0.3288 (t80) REVERT: D 186 LEU cc_start: 0.0512 (OUTLIER) cc_final: 0.0171 (tp) REVERT: E 207 THR cc_start: 0.3635 (OUTLIER) cc_final: 0.2976 (m) REVERT: F 6 GLN cc_start: 0.5550 (pp30) cc_final: 0.5279 (mp10) REVERT: F 7 MET cc_start: 0.4231 (tmm) cc_final: 0.3744 (tmm) REVERT: F 74 PHE cc_start: 0.4879 (m-80) cc_final: 0.4550 (m-80) REVERT: G 45 LEU cc_start: 0.5421 (OUTLIER) cc_final: 0.4855 (tt) REVERT: G 83 MET cc_start: 0.5243 (mtm) cc_final: 0.4978 (mtm) REVERT: G 194 LEU cc_start: 0.0318 (mt) cc_final: 0.0055 (mt) REVERT: I 32 TYR cc_start: 0.6679 (m-80) cc_final: 0.6427 (m-80) REVERT: I 87 ARG cc_start: 0.6435 (mtm110) cc_final: 0.5998 (mtm110) REVERT: I 192 TYR cc_start: 0.5478 (m-80) cc_final: 0.5222 (m-80) outliers start: 140 outliers final: 96 residues processed: 324 average time/residue: 0.4210 time to fit residues: 232.9654 Evaluate side-chains 286 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 180 time to evaluate : 3.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1184 TRP Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 797 THR Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1055 ILE Chi-restraints excluded: chain C residue 1059 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1089 SER Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 138 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 430 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 325 optimal weight: 1.9990 chunk 252 optimal weight: 9.9990 chunk 375 optimal weight: 1.9990 chunk 249 optimal weight: 8.9990 chunk 444 optimal weight: 20.0000 chunk 278 optimal weight: 5.9990 chunk 270 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 264 HIS ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 ASN ** C1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN ** H 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5642 moved from start: 0.7013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35159 Z= 0.282 Angle : 0.708 8.923 47932 Z= 0.375 Chirality : 0.045 0.253 5550 Planarity : 0.005 0.052 6205 Dihedral : 6.436 59.428 5011 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.43 % Favored : 92.24 % Rotamer: Outliers : 4.68 % Allowed : 18.37 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.35 (0.12), residues: 4595 helix: 0.71 (0.19), residues: 762 sheet: -0.14 (0.15), residues: 1239 loop : -1.85 (0.11), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 553 HIS 0.008 0.002 HIS A1138 PHE 0.048 0.003 PHE C1044 TYR 0.034 0.002 TYR B 85 ARG 0.012 0.001 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 195 time to evaluate : 3.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 PHE cc_start: 0.3718 (m-80) cc_final: 0.3412 (m-80) REVERT: A 523 TYR cc_start: 0.4111 (m-80) cc_final: 0.3548 (m-10) REVERT: A 549 GLU cc_start: 0.4065 (OUTLIER) cc_final: 0.3488 (tp30) REVERT: A 795 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8209 (mm) REVERT: A 1003 GLN cc_start: 0.7569 (mt0) cc_final: 0.6716 (tm-30) REVERT: A 1012 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.7029 (t80) REVERT: B 438 TYR cc_start: 0.5071 (m-80) cc_final: 0.4562 (m-80) REVERT: B 505 ARG cc_start: 0.3714 (tmt170) cc_final: 0.3005 (ttp-110) REVERT: B 662 ILE cc_start: 0.6652 (OUTLIER) cc_final: 0.6386 (tp) REVERT: B 977 PHE cc_start: 0.7748 (m-10) cc_final: 0.7460 (m-10) REVERT: B 988 GLN cc_start: 0.6863 (mm110) cc_final: 0.6314 (pt0) REVERT: C 517 LEU cc_start: 0.6030 (pt) cc_final: 0.4741 (mt) REVERT: D 186 LEU cc_start: 0.0641 (OUTLIER) cc_final: 0.0282 (tp) REVERT: E 32 TYR cc_start: 0.5949 (OUTLIER) cc_final: 0.4624 (m-80) REVERT: E 207 THR cc_start: 0.3433 (OUTLIER) cc_final: 0.2729 (m) REVERT: F 7 MET cc_start: 0.4163 (tmm) cc_final: 0.3752 (tmm) REVERT: F 74 PHE cc_start: 0.4856 (m-80) cc_final: 0.4514 (m-80) REVERT: G 83 MET cc_start: 0.5404 (mtm) cc_final: 0.5182 (mtm) REVERT: G 194 LEU cc_start: 0.0495 (mt) cc_final: 0.0175 (mt) REVERT: H 29 SER cc_start: 0.2056 (OUTLIER) cc_final: 0.1577 (p) REVERT: I 32 TYR cc_start: 0.6872 (m-80) cc_final: 0.6642 (m-80) REVERT: I 87 ARG cc_start: 0.6486 (mtm110) cc_final: 0.6075 (mtm110) REVERT: I 192 TYR cc_start: 0.5476 (m-80) cc_final: 0.5225 (m-80) outliers start: 171 outliers final: 131 residues processed: 349 average time/residue: 0.4187 time to fit residues: 249.0837 Evaluate side-chains 316 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 177 time to evaluate : 3.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 797 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1059 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1089 SER Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1156 CYS Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 92 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 139 CYS Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 138 PHE Chi-restraints excluded: chain I residue 194 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 274 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 chunk 265 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 282 optimal weight: 0.9990 chunk 302 optimal weight: 1.9990 chunk 219 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 349 optimal weight: 0.0040 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN C 319 GLN C 398 ASN C 521 ASN ** C 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1160 ASN D 6 GLN ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN ** H 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5574 moved from start: 0.7018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35159 Z= 0.174 Angle : 0.620 10.069 47932 Z= 0.324 Chirality : 0.043 0.178 5550 Planarity : 0.004 0.055 6205 Dihedral : 5.804 57.792 5008 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.86 % Favored : 93.88 % Rotamer: Outliers : 3.15 % Allowed : 19.88 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.12 (0.12), residues: 4595 helix: 1.10 (0.19), residues: 775 sheet: 0.11 (0.15), residues: 1139 loop : -1.79 (0.11), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 553 HIS 0.004 0.001 HIS E 35 PHE 0.052 0.002 PHE C1044 TYR 0.033 0.002 TYR B 105 ARG 0.009 0.001 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 193 time to evaluate : 4.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6470 (ptp-170) REVERT: A 385 PHE cc_start: 0.3698 (m-80) cc_final: 0.3236 (m-80) REVERT: A 523 TYR cc_start: 0.4152 (m-80) cc_final: 0.3617 (m-10) REVERT: A 553 TRP cc_start: 0.2128 (t-100) cc_final: 0.1733 (t-100) REVERT: A 795 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.7993 (mm) REVERT: A 833 GLN cc_start: 0.7815 (mt0) cc_final: 0.7537 (mt0) REVERT: A 1012 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6979 (t80) REVERT: B 505 ARG cc_start: 0.3692 (tmt170) cc_final: 0.3343 (ttp-170) REVERT: B 620 CYS cc_start: 0.2767 (OUTLIER) cc_final: 0.2561 (m) REVERT: B 662 ILE cc_start: 0.6563 (OUTLIER) cc_final: 0.6232 (tp) REVERT: B 686 MET cc_start: 0.4285 (ttp) cc_final: 0.4053 (ttp) REVERT: B 977 PHE cc_start: 0.7811 (m-10) cc_final: 0.7490 (m-10) REVERT: B 988 GLN cc_start: 0.6946 (mm-40) cc_final: 0.6213 (pt0) REVERT: C 517 LEU cc_start: 0.5914 (pt) cc_final: 0.4653 (mt) REVERT: C 641 TYR cc_start: 0.3135 (OUTLIER) cc_final: 0.0708 (p90) REVERT: C 938 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7831 (tp) REVERT: D 52 TYR cc_start: 0.4897 (t80) cc_final: 0.3242 (t80) REVERT: D 186 LEU cc_start: 0.0577 (OUTLIER) cc_final: 0.0253 (tp) REVERT: E 191 LEU cc_start: 0.0197 (OUTLIER) cc_final: -0.0040 (mt) REVERT: E 207 THR cc_start: 0.3473 (OUTLIER) cc_final: 0.2880 (m) REVERT: F 7 MET cc_start: 0.4155 (tmm) cc_final: 0.3782 (tmm) REVERT: F 74 PHE cc_start: 0.4702 (m-80) cc_final: 0.4384 (m-80) REVERT: F 103 PHE cc_start: 0.6033 (p90) cc_final: 0.5561 (p90) REVERT: G 83 MET cc_start: 0.5401 (mtm) cc_final: 0.4935 (mtt) REVERT: G 194 LEU cc_start: 0.0421 (mt) cc_final: 0.0085 (mt) REVERT: I 87 ARG cc_start: 0.6463 (mtm110) cc_final: 0.6049 (mtm110) REVERT: I 192 TYR cc_start: 0.5458 (m-80) cc_final: 0.5214 (m-80) outliers start: 115 outliers final: 87 residues processed: 300 average time/residue: 0.4331 time to fit residues: 219.2833 Evaluate side-chains 275 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 178 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1055 ILE Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1089 SER Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 138 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 404 optimal weight: 0.7980 chunk 425 optimal weight: 30.0000 chunk 388 optimal weight: 9.9990 chunk 414 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 180 optimal weight: 0.4980 chunk 325 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 374 optimal weight: 20.0000 chunk 391 optimal weight: 8.9990 chunk 412 optimal weight: 7.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5670 moved from start: 0.7432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 35159 Z= 0.292 Angle : 0.719 9.371 47932 Z= 0.380 Chirality : 0.045 0.249 5550 Planarity : 0.005 0.062 6205 Dihedral : 6.279 59.958 5005 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.48 % Favored : 91.24 % Rotamer: Outliers : 3.78 % Allowed : 19.44 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.44 (0.12), residues: 4595 helix: 0.68 (0.18), residues: 779 sheet: -0.13 (0.15), residues: 1154 loop : -1.94 (0.11), residues: 2662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 553 HIS 0.009 0.002 HIS A1138 PHE 0.050 0.003 PHE C1044 TYR 0.050 0.002 TYR B 105 ARG 0.017 0.001 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 188 time to evaluate : 3.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6538 (ptp-170) REVERT: A 278 MET cc_start: 0.8067 (mmp) cc_final: 0.7774 (mmt) REVERT: A 385 PHE cc_start: 0.3637 (m-80) cc_final: 0.3294 (m-80) REVERT: A 523 TYR cc_start: 0.4143 (m-80) cc_final: 0.3593 (m-10) REVERT: A 549 GLU cc_start: 0.4023 (OUTLIER) cc_final: 0.3461 (tp30) REVERT: A 795 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8209 (mm) REVERT: A 985 ILE cc_start: 0.5486 (OUTLIER) cc_final: 0.5208 (pt) REVERT: A 1003 GLN cc_start: 0.7505 (mt0) cc_final: 0.6672 (tm-30) REVERT: A 1012 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.7022 (t80) REVERT: B 240 MET cc_start: 0.6427 (mpp) cc_final: 0.5966 (mpp) REVERT: B 505 ARG cc_start: 0.3706 (tmt170) cc_final: 0.3009 (ttp-110) REVERT: B 662 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.6362 (tp) REVERT: B 686 MET cc_start: 0.4335 (ttp) cc_final: 0.4029 (ttp) REVERT: B 977 PHE cc_start: 0.7799 (m-10) cc_final: 0.7505 (m-10) REVERT: B 988 GLN cc_start: 0.7200 (mm-40) cc_final: 0.6302 (tt0) REVERT: C 517 LEU cc_start: 0.5969 (pt) cc_final: 0.4691 (mt) REVERT: E 32 TYR cc_start: 0.6070 (OUTLIER) cc_final: 0.4687 (m-80) REVERT: E 87 ARG cc_start: 0.7414 (mpp80) cc_final: 0.6929 (mmp80) REVERT: E 191 LEU cc_start: -0.0186 (OUTLIER) cc_final: -0.0459 (mt) REVERT: E 207 THR cc_start: 0.3064 (OUTLIER) cc_final: 0.2390 (m) REVERT: F 74 PHE cc_start: 0.4834 (m-80) cc_final: 0.4480 (m-80) REVERT: G 83 MET cc_start: 0.5400 (mtm) cc_final: 0.4993 (mtt) REVERT: G 194 LEU cc_start: 0.0516 (mt) cc_final: 0.0173 (mt) REVERT: H 29 SER cc_start: 0.2036 (OUTLIER) cc_final: 0.1577 (p) REVERT: H 175 ASP cc_start: 0.5497 (OUTLIER) cc_final: 0.5252 (m-30) REVERT: I 34 MET cc_start: 0.4318 (tpp) cc_final: 0.3999 (tpt) REVERT: I 87 ARG cc_start: 0.6528 (mtm110) cc_final: 0.6178 (mtm110) REVERT: I 192 TYR cc_start: 0.5506 (m-80) cc_final: 0.5265 (m-80) outliers start: 138 outliers final: 109 residues processed: 315 average time/residue: 0.4631 time to fit residues: 247.8066 Evaluate side-chains 296 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 176 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1089 SER Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 175 ASP Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 138 PHE Chi-restraints excluded: chain I residue 143 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 271 optimal weight: 2.9990 chunk 437 optimal weight: 20.0000 chunk 267 optimal weight: 0.4980 chunk 207 optimal weight: 0.8980 chunk 304 optimal weight: 8.9990 chunk 459 optimal weight: 20.0000 chunk 422 optimal weight: 6.9990 chunk 365 optimal weight: 20.0000 chunk 37 optimal weight: 0.4980 chunk 282 optimal weight: 0.0030 chunk 224 optimal weight: 2.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 981 ASN C 521 ASN ** C 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5594 moved from start: 0.7393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35159 Z= 0.177 Angle : 0.632 10.167 47932 Z= 0.328 Chirality : 0.043 0.234 5550 Planarity : 0.004 0.047 6205 Dihedral : 5.741 58.337 5005 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.36 % Favored : 93.35 % Rotamer: Outliers : 2.88 % Allowed : 20.43 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.18 (0.12), residues: 4595 helix: 1.13 (0.19), residues: 782 sheet: 0.00 (0.15), residues: 1161 loop : -1.84 (0.11), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 553 HIS 0.004 0.001 HIS E 35 PHE 0.051 0.002 PHE C1044 TYR 0.053 0.002 TYR B 641 ARG 0.008 0.001 ARG B 694 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 188 time to evaluate : 4.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6553 (ptp-170) REVERT: A 278 MET cc_start: 0.7995 (mmp) cc_final: 0.7719 (mmt) REVERT: A 385 PHE cc_start: 0.3643 (m-80) cc_final: 0.3228 (m-80) REVERT: A 523 TYR cc_start: 0.4044 (m-80) cc_final: 0.3522 (m-10) REVERT: A 549 GLU cc_start: 0.4457 (OUTLIER) cc_final: 0.3866 (tp30) REVERT: A 553 TRP cc_start: 0.2021 (t-100) cc_final: 0.1574 (t-100) REVERT: A 563 MET cc_start: 0.3892 (mmp) cc_final: 0.3629 (mmt) REVERT: A 795 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.7958 (mm) REVERT: A 833 GLN cc_start: 0.7845 (mt0) cc_final: 0.7548 (mt0) REVERT: A 985 ILE cc_start: 0.5799 (OUTLIER) cc_final: 0.5152 (pt) REVERT: A 1012 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6985 (t80) REVERT: B 505 ARG cc_start: 0.3497 (tmt170) cc_final: 0.3181 (ttp-170) REVERT: B 662 ILE cc_start: 0.6557 (OUTLIER) cc_final: 0.6211 (tp) REVERT: B 977 PHE cc_start: 0.7834 (m-10) cc_final: 0.7538 (m-10) REVERT: B 988 GLN cc_start: 0.7133 (mm-40) cc_final: 0.6359 (pt0) REVERT: C 517 LEU cc_start: 0.6068 (pt) cc_final: 0.4874 (mt) REVERT: C 641 TYR cc_start: 0.3313 (OUTLIER) cc_final: 0.0970 (p90) REVERT: C 938 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7700 (tp) REVERT: D 7 MET cc_start: 0.4242 (tmm) cc_final: 0.3269 (mmm) REVERT: E 191 LEU cc_start: -0.0151 (OUTLIER) cc_final: -0.0411 (mt) REVERT: E 207 THR cc_start: 0.3424 (OUTLIER) cc_final: 0.2823 (m) REVERT: F 6 GLN cc_start: 0.5905 (pp30) cc_final: 0.5633 (pm20) REVERT: F 7 MET cc_start: 0.4237 (tmm) cc_final: 0.3896 (tmm) REVERT: G 68 PHE cc_start: 0.1960 (m-80) cc_final: 0.1588 (m-80) REVERT: G 83 MET cc_start: 0.5451 (mtm) cc_final: 0.5056 (mtt) REVERT: G 194 LEU cc_start: 0.0489 (mt) cc_final: 0.0177 (mt) REVERT: H 29 SER cc_start: 0.1683 (OUTLIER) cc_final: 0.1290 (p) REVERT: I 192 TYR cc_start: 0.5532 (m-80) cc_final: 0.5297 (m-80) outliers start: 105 outliers final: 78 residues processed: 283 average time/residue: 0.4756 time to fit residues: 229.3645 Evaluate side-chains 261 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 172 time to evaluate : 3.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1089 SER Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 194 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 290 optimal weight: 10.0000 chunk 389 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 337 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 366 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 376 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 981 ASN ** C1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.100755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.081199 restraints weight = 434300.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.079129 restraints weight = 335923.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.078989 restraints weight = 419612.338| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.7645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 35159 Z= 0.248 Angle : 0.679 10.419 47932 Z= 0.356 Chirality : 0.044 0.241 5550 Planarity : 0.005 0.053 6205 Dihedral : 5.988 59.651 5003 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.15 % Favored : 91.59 % Rotamer: Outliers : 3.09 % Allowed : 20.26 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.34 (0.12), residues: 4595 helix: 0.92 (0.19), residues: 782 sheet: -0.15 (0.15), residues: 1172 loop : -1.90 (0.11), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 553 HIS 0.007 0.001 HIS A1138 PHE 0.050 0.002 PHE C1044 TYR 0.061 0.002 TYR B 642 ARG 0.011 0.001 ARG C 401 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7073.52 seconds wall clock time: 127 minutes 54.26 seconds (7674.26 seconds total)