Starting phenix.real_space_refine on Tue Feb 20 01:15:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kl9_22916/02_2024/7kl9_22916.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kl9_22916/02_2024/7kl9_22916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kl9_22916/02_2024/7kl9_22916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kl9_22916/02_2024/7kl9_22916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kl9_22916/02_2024/7kl9_22916.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kl9_22916/02_2024/7kl9_22916.pdb" } resolution = 4.1 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= 0.019 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 110 5.16 5 C 16803 2.51 5 N 4454 2.21 5 O 4991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 808": "OD1" <-> "OD2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 737": "OD1" <-> "OD2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E GLU 43": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "F ASP 5": "OD1" <-> "OD2" Residue "F ASP 10": "OD1" <-> "OD2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ARG 42": "NH1" <-> "NH2" Residue "F TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 134": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26358 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7433 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 53, 'TRANS': 941} Chain breaks: 8 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 13, 'ASP:plan': 17, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 192 Chain: "B" Number of atoms: 7435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7435 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 276 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 14, 'ASP:plan': 17, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 203 Chain: "C" Number of atoms: 7435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7435 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 53, 'TRANS': 941} Chain breaks: 8 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 421 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 13, 'ASP:plan': 17, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 183 Chain: "E" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1207 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'TRANS': 159} Chain: "D" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1207 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'TRANS': 159} Chain: "F" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1207 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'TRANS': 159} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.36, per 1000 atoms: 0.51 Number of scatterers: 26358 At special positions: 0 Unit cell: (134.695, 158.158, 203.346, 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 110 16.00 O 4991 8.00 N 4454 7.00 C 16803 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 331 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 122 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 331 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 122 " " NAG C1308 " - " ASN C 709 " " NAG G 1 " - " ASN C 165 " " NAG H 1 " - " ASN C 331 " Time building additional restraints: 11.10 Conformation dependent library (CDL) restraints added in 4.7 seconds 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6528 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 46 sheets defined 33.3% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.551A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.288A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.252A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.909A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.568A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.876A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.588A pdb=" N ALA A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.552A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.306A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.272A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.629A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.145A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 343' Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.552A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 738 through 743 removed outlier: 3.512A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.104A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 885 through 890 removed outlier: 3.623A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.602A pdb=" N GLN B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.020A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.564A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.580A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.887A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.726A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.580A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.209A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 removed outlier: 4.105A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.629A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.581A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.233A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.709A pdb=" N GLN C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.319A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.505A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.360A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'E' and resid 17 through 48 removed outlier: 3.968A pdb=" N ARG E 21 " --> pdb=" O SER E 17 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE E 40 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 82 removed outlier: 3.729A pdb=" N GLU E 56 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA E 71 " --> pdb=" O LYS E 67 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA E 76 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 117 removed outlier: 4.444A pdb=" N ALA E 107 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU E 116 " --> pdb=" O MET E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 156 removed outlier: 3.648A pdb=" N PHE E 132 " --> pdb=" O GLN E 128 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA E 133 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS E 135 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP E 142 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE E 152 " --> pdb=" O ALA E 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 35 removed outlier: 3.868A pdb=" N ALA D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 46 removed outlier: 3.577A pdb=" N ILE D 40 " --> pdb=" O GLU D 36 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ILE D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 79 removed outlier: 3.766A pdb=" N ALA D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 83 Processing helix chain 'D' and resid 85 through 95 removed outlier: 3.763A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 114 removed outlier: 4.176A pdb=" N GLU D 101 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 108 " --> pdb=" O GLU D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 151 removed outlier: 4.090A pdb=" N LYS D 130 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN D 146 " --> pdb=" O ASP D 142 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA D 150 " --> pdb=" O GLN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'F' and resid 6 through 10 Processing helix chain 'F' and resid 17 through 26 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 30 through 46 removed outlier: 3.505A pdb=" N LYS F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU F 39 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU F 46 " --> pdb=" O ARG F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 83 removed outlier: 4.268A pdb=" N GLU F 56 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU F 74 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 82 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 89 through 120 removed outlier: 3.589A pdb=" N GLU F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 116 " --> pdb=" O MET F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 158 removed outlier: 3.836A pdb=" N ASP F 134 " --> pdb=" O LYS F 130 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE F 152 " --> pdb=" O ALA F 148 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.533A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.206A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.673A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 318 removed outlier: 6.851A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.718A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.111A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.647A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.879A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.709A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 719 removed outlier: 3.988A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 722 through 728 removed outlier: 3.962A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.397A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.015A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.641A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.292A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 160 through 164 removed outlier: 3.787A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 314 through 319 removed outlier: 5.783A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 376 through 377 Processing sheet with id=AC4, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 541 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 656 removed outlier: 4.859A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.738A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.738A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD1, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 3.526A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.613A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.947A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 103 through 106 removed outlier: 5.978A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 201 through 205 removed outlier: 4.874A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.330A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.547A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.626A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.394A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.576A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.576A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AE8, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 3.638A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.985A pdb=" N ILE E 4 " --> pdb=" O ARG E 12 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 4 through 6 removed outlier: 4.473A pdb=" N ILE D 4 " --> pdb=" O ARG D 12 " (cutoff:3.500A) 1077 hydrogen bonds defined for protein. 2988 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: 11.81 Time building geometry restraints manager: 11.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6063 1.33 - 1.45: 6674 1.45 - 1.58: 14018 1.58 - 1.70: 0 1.70 - 1.83: 143 Bond restraints: 26898 Sorted by residual: bond pdb=" N ARG C 328 " pdb=" CA ARG C 328 " ideal model delta sigma weight residual 1.457 1.529 -0.072 1.53e-02 4.27e+03 2.24e+01 bond pdb=" C VAL B 860 " pdb=" N LEU B 861 " ideal model delta sigma weight residual 1.331 1.201 0.130 2.83e-02 1.25e+03 2.11e+01 bond pdb=" N PRO C 330 " pdb=" CA PRO C 330 " ideal model delta sigma weight residual 1.469 1.527 -0.059 1.28e-02 6.10e+03 2.11e+01 bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.457 1.519 -0.062 1.41e-02 5.03e+03 1.92e+01 bond pdb=" CA PHE C 329 " pdb=" C PHE C 329 " ideal model delta sigma weight residual 1.524 1.574 -0.050 1.26e-02 6.30e+03 1.57e+01 ... (remaining 26893 not shown) Histogram of bond angle deviations from ideal: 95.97 - 103.61: 386 103.61 - 111.24: 11191 111.24 - 118.88: 10044 118.88 - 126.51: 14744 126.51 - 134.15: 255 Bond angle restraints: 36620 Sorted by residual: angle pdb=" CA PRO C 384 " pdb=" N PRO C 384 " pdb=" CD PRO C 384 " ideal model delta sigma weight residual 112.00 99.45 12.55 1.40e+00 5.10e-01 8.04e+01 angle pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 112.00 99.69 12.31 1.40e+00 5.10e-01 7.73e+01 angle pdb=" N ARG C 328 " pdb=" CA ARG C 328 " pdb=" C ARG C 328 " ideal model delta sigma weight residual 108.34 119.52 -11.18 1.31e+00 5.83e-01 7.28e+01 angle pdb=" N PRO C 330 " pdb=" CA PRO C 330 " pdb=" C PRO C 330 " ideal model delta sigma weight residual 112.47 127.71 -15.24 2.06e+00 2.36e-01 5.47e+01 angle pdb=" C PHE C 329 " pdb=" N PRO C 330 " pdb=" CA PRO C 330 " ideal model delta sigma weight residual 119.84 128.52 -8.68 1.25e+00 6.40e-01 4.82e+01 ... (remaining 36615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15023 17.95 - 35.90: 1195 35.90 - 53.86: 190 53.86 - 71.81: 43 71.81 - 89.76: 28 Dihedral angle restraints: 16479 sinusoidal: 6375 harmonic: 10104 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -161.43 75.43 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 35.81 57.19 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CA CYS A 760 " pdb=" C CYS A 760 " pdb=" N THR A 761 " pdb=" CA THR A 761 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 16476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 4207 0.132 - 0.264: 67 0.264 - 0.396: 3 0.396 - 0.528: 3 0.528 - 0.660: 2 Chirality restraints: 4282 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-02 2.50e+03 1.09e+03 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 4279 not shown) Planarity restraints: 4787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.292 2.00e-02 2.50e+03 2.47e-01 7.63e+02 pdb=" C7 NAG H 1 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.425 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.277 2.00e-02 2.50e+03 2.32e-01 6.75e+02 pdb=" C7 NAG H 2 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.182 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.393 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1311 " -0.160 2.00e-02 2.50e+03 1.32e-01 2.18e+02 pdb=" C7 NAG B1311 " 0.044 2.00e-02 2.50e+03 pdb=" C8 NAG B1311 " -0.119 2.00e-02 2.50e+03 pdb=" N2 NAG B1311 " 0.212 2.00e-02 2.50e+03 pdb=" O7 NAG B1311 " 0.022 2.00e-02 2.50e+03 ... (remaining 4784 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 3 1.97 - 2.70: 1624 2.70 - 3.44: 42107 3.44 - 4.17: 63266 4.17 - 4.90: 107496 Nonbonded interactions: 214496 Sorted by model distance: nonbonded pdb=" OE2 GLU C 406 " pdb=" OH TYR C 495 " model vdw 1.240 2.440 nonbonded pdb=" CD2 PHE C 374 " pdb=" CG2 ILE C 434 " model vdw 1.871 3.760 nonbonded pdb=" CD GLU C 406 " pdb=" OH TYR C 495 " model vdw 1.921 3.270 nonbonded pdb=" NH1 ARG B 328 " pdb=" O ASN B 532 " model vdw 2.020 2.520 nonbonded pdb=" OG1 THR C 323 " pdb=" NZ LYS C 537 " model vdw 2.054 2.520 ... (remaining 214491 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 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 166 or (resid 167 through 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 333 or \ (resid 334 through 336 and (name N or name CA or name C or name O or name CB )) \ or resid 337 through 416 or (resid 417 and (name N or name CA or name C or name \ O or name CB )) or resid 418 through 443 or (resid 444 and (name N or name CA o \ r name C or name O or name CB )) or resid 445 through 920 or (resid 921 and (nam \ e N or name CA or name C or name O or name CB )) or resid 922 through 1145 or re \ sid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 402 or (resid 403 and (name N or name CA or nam \ e C or name O or name CB )) or resid 404 through 405 or (resid 406 and (name N o \ r name CA or name C or name O or name CB )) or resid 407 through 416 or (resid 4 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 418 through \ 443 or (resid 444 and (name N or name CA or name C or name O or name CB )) or r \ esid 445 through 516 or resid 520 through 1145 or resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 166 or (resid 167 through 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 333 or \ (resid 334 through 336 and (name N or name CA or name C or name O or name CB )) \ or resid 337 through 402 or (resid 403 and (name N or name CA or name C or name \ O or name CB )) or resid 404 through 405 or (resid 406 and (name N or name CA o \ r name C or name O or name CB )) or resid 407 through 920 or (resid 921 and (nam \ e N or name CA or name C or name O or name CB )) or resid 922 through 1145 or re \ sid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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=1.00 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: 4.350 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: 0.020 Extract box with map and model: 19.110 Check model and map are aligned: 0.440 Set scattering table: 0.240 Process input model: 70.770 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 : 0.009 0.130 26898 Z= 0.566 Angle : 0.903 15.647 36620 Z= 0.493 Chirality : 0.056 0.660 4282 Planarity : 0.008 0.247 4758 Dihedral : 13.709 89.762 9849 Min Nonbonded Distance : 1.240 Molprobity Statistics. All-atom Clashscore : 30.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.85 % Favored : 87.95 % Rotamer: Outliers : 0.27 % Allowed : 0.59 % Favored : 99.14 % Cbeta Deviations : 0.06 % 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: -2.99 (0.13), residues: 3410 helix: -1.63 (0.15), residues: 894 sheet: -1.55 (0.21), residues: 545 loop : -2.35 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 886 HIS 0.010 0.002 HIS A 655 PHE 0.041 0.003 PHE B 275 TYR 0.030 0.003 TYR A 904 ARG 0.009 0.001 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 172 time to evaluate : 2.955 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 433 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8144 (t) REVERT: B 160 TYR cc_start: 0.7899 (p90) cc_final: 0.7326 (p90) REVERT: B 201 PHE cc_start: 0.9098 (t80) cc_final: 0.8854 (t80) REVERT: C 104 TRP cc_start: 0.7647 (m-90) cc_final: 0.7438 (m-90) REVERT: C 390 LEU cc_start: 0.8473 (tp) cc_final: 0.8247 (tp) REVERT: C 740 MET cc_start: 0.8019 (tpt) cc_final: 0.7700 (tpp) REVERT: E 34 MET cc_start: 0.7389 (tmm) cc_final: 0.7170 (mtp) REVERT: E 140 MET cc_start: 0.8830 (mmp) cc_final: 0.8110 (mmp) REVERT: D 109 LEU cc_start: 0.3933 (mt) cc_final: 0.3636 (mt) REVERT: D 140 MET cc_start: 0.5570 (ptt) cc_final: 0.4681 (mtt) outliers start: 7 outliers final: 5 residues processed: 178 average time/residue: 0.3540 time to fit residues: 103.1353 Evaluate side-chains 106 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 270 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 313 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 913 GLN B 519 HIS ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26898 Z= 0.241 Angle : 0.686 12.592 36620 Z= 0.364 Chirality : 0.049 0.463 4282 Planarity : 0.005 0.080 4758 Dihedral : 7.451 58.368 4355 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.74 % Favored : 92.20 % Rotamer: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.64 % Cbeta Deviations : 0.00 % 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: -2.21 (0.14), residues: 3410 helix: -0.48 (0.16), residues: 966 sheet: -1.19 (0.22), residues: 498 loop : -2.14 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 104 HIS 0.012 0.001 HIS E 138 PHE 0.056 0.002 PHE F 144 TYR 0.031 0.002 TYR F 113 ARG 0.006 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 169 time to evaluate : 3.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8807 (ptt) cc_final: 0.8594 (ptm) REVERT: A 777 ASN cc_start: 0.9424 (m-40) cc_final: 0.8928 (m110) REVERT: A 1005 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8395 (tm-30) REVERT: B 160 TYR cc_start: 0.7676 (p90) cc_final: 0.7147 (p90) REVERT: C 346 ARG cc_start: 0.6347 (tmt170) cc_final: 0.5907 (tmt170) REVERT: C 697 MET cc_start: 0.8549 (ppp) cc_final: 0.8091 (ppp) REVERT: C 740 MET cc_start: 0.7640 (tpt) cc_final: 0.7376 (tpp) REVERT: C 777 ASN cc_start: 0.8704 (m110) cc_final: 0.8334 (m110) REVERT: E 34 MET cc_start: 0.6918 (tmm) cc_final: 0.6693 (mtp) REVERT: E 72 ILE cc_start: 0.8555 (pt) cc_final: 0.8327 (pt) REVERT: E 140 MET cc_start: 0.8754 (mmp) cc_final: 0.8370 (mmt) REVERT: D 140 MET cc_start: 0.5670 (ptt) cc_final: 0.4591 (mtt) REVERT: F 132 PHE cc_start: 0.8043 (p90) cc_final: 0.7590 (t80) outliers start: 3 outliers final: 1 residues processed: 172 average time/residue: 0.3590 time to fit residues: 103.2053 Evaluate side-chains 104 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 0.6980 chunk 97 optimal weight: 0.0670 chunk 260 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 313 optimal weight: 1.9990 chunk 339 optimal weight: 20.0000 chunk 279 optimal weight: 8.9990 chunk 311 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 251 optimal weight: 0.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1113 GLN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26898 Z= 0.194 Angle : 0.606 11.724 36620 Z= 0.316 Chirality : 0.047 0.468 4282 Planarity : 0.004 0.053 4758 Dihedral : 6.552 59.915 4355 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.72 % Favored : 93.23 % Rotamer: Outliers : 0.08 % Allowed : 5.40 % Favored : 94.52 % Cbeta Deviations : 0.00 % 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: -1.89 (0.14), residues: 3410 helix: -0.26 (0.16), residues: 987 sheet: -0.95 (0.21), residues: 549 loop : -1.95 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 436 HIS 0.012 0.001 HIS E 138 PHE 0.037 0.002 PHE F 144 TYR 0.030 0.001 TYR F 113 ARG 0.003 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.7507 (m-80) cc_final: 0.7051 (m-10) REVERT: A 777 ASN cc_start: 0.9368 (m-40) cc_final: 0.9152 (m110) REVERT: A 1005 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8209 (tm-30) REVERT: B 160 TYR cc_start: 0.7395 (p90) cc_final: 0.7025 (p90) REVERT: B 996 LEU cc_start: 0.9673 (tp) cc_final: 0.9447 (tt) REVERT: C 697 MET cc_start: 0.8606 (ppp) cc_final: 0.8266 (ppp) REVERT: C 777 ASN cc_start: 0.8845 (m110) cc_final: 0.8435 (m110) REVERT: E 34 MET cc_start: 0.7080 (tmm) cc_final: 0.6760 (mtp) REVERT: E 72 ILE cc_start: 0.8632 (pt) cc_final: 0.8175 (pt) REVERT: E 91 ASN cc_start: 0.9315 (m110) cc_final: 0.9009 (m110) REVERT: E 140 MET cc_start: 0.8717 (mmp) cc_final: 0.7981 (mmt) REVERT: E 144 PHE cc_start: 0.7952 (m-10) cc_final: 0.7713 (m-10) REVERT: D 140 MET cc_start: 0.5327 (ptt) cc_final: 0.3867 (mtt) REVERT: F 34 MET cc_start: 0.2694 (mpp) cc_final: 0.2367 (tpp) outliers start: 2 outliers final: 0 residues processed: 197 average time/residue: 0.3375 time to fit residues: 112.2774 Evaluate side-chains 114 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 9.9990 chunk 235 optimal weight: 0.4980 chunk 162 optimal weight: 6.9990 chunk 34 optimal weight: 0.3980 chunk 149 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 chunk 314 optimal weight: 0.8980 chunk 333 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 overall best weight: 3.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 487 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1054 GLN C1142 GLN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26898 Z= 0.314 Angle : 0.652 11.722 36620 Z= 0.339 Chirality : 0.047 0.461 4282 Planarity : 0.004 0.051 4758 Dihedral : 6.524 58.879 4355 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.09 % Favored : 91.85 % Rotamer: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.27 % Cbeta Deviations : 0.00 % 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: -1.83 (0.14), residues: 3410 helix: -0.11 (0.16), residues: 995 sheet: -0.89 (0.21), residues: 552 loop : -1.99 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 436 HIS 0.009 0.002 HIS E 138 PHE 0.039 0.002 PHE D 144 TYR 0.026 0.002 TYR F 113 ARG 0.016 0.001 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.7504 (m-80) cc_final: 0.7253 (m-10) REVERT: A 697 MET cc_start: 0.8852 (ptt) cc_final: 0.8620 (ptm) REVERT: A 777 ASN cc_start: 0.9449 (m-40) cc_final: 0.9059 (m110) REVERT: A 1005 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8402 (tm-30) REVERT: B 160 TYR cc_start: 0.7481 (p90) cc_final: 0.7137 (p90) REVERT: B 313 TYR cc_start: 0.9011 (m-80) cc_final: 0.8296 (m-80) REVERT: B 882 ILE cc_start: 0.9348 (mt) cc_final: 0.9130 (tt) REVERT: B 1050 MET cc_start: 0.8242 (ptp) cc_final: 0.7842 (ptp) REVERT: C 464 PHE cc_start: 0.6270 (m-10) cc_final: 0.5471 (p90) REVERT: C 697 MET cc_start: 0.8735 (ppp) cc_final: 0.8282 (ppp) REVERT: E 34 MET cc_start: 0.7079 (tmm) cc_final: 0.6727 (mtp) REVERT: E 72 ILE cc_start: 0.8691 (pt) cc_final: 0.8199 (pt) REVERT: E 91 ASN cc_start: 0.9326 (m110) cc_final: 0.9085 (m-40) REVERT: E 140 MET cc_start: 0.8814 (mmp) cc_final: 0.8052 (mmt) REVERT: E 144 PHE cc_start: 0.7959 (m-10) cc_final: 0.7577 (m-10) REVERT: D 49 ARG cc_start: 0.5839 (tpm170) cc_final: 0.5411 (tpt90) REVERT: D 140 MET cc_start: 0.5078 (ptt) cc_final: 0.4592 (ptt) REVERT: F 34 MET cc_start: 0.2883 (mpp) cc_final: 0.2588 (mpp) outliers start: 1 outliers final: 1 residues processed: 171 average time/residue: 0.3369 time to fit residues: 96.8618 Evaluate side-chains 109 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 0.0770 chunk 189 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 284 optimal weight: 0.8980 chunk 230 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 299 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 overall best weight: 3.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN C1142 GLN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 26898 Z= 0.307 Angle : 0.642 11.802 36620 Z= 0.333 Chirality : 0.047 0.436 4282 Planarity : 0.004 0.053 4758 Dihedral : 6.439 58.557 4355 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.15 % Favored : 91.79 % Rotamer: Outliers : 0.04 % Allowed : 4.19 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.76 (0.14), residues: 3410 helix: 0.00 (0.16), residues: 1002 sheet: -0.84 (0.22), residues: 545 loop : -2.00 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 436 HIS 0.011 0.001 HIS E 138 PHE 0.029 0.002 PHE F 144 TYR 0.038 0.002 TYR C 873 ARG 0.006 0.001 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.7480 (m-80) cc_final: 0.7199 (m-10) REVERT: A 1005 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8536 (tm-30) REVERT: A 1048 HIS cc_start: 0.8645 (t-90) cc_final: 0.8433 (t70) REVERT: B 160 TYR cc_start: 0.7523 (p90) cc_final: 0.7247 (p90) REVERT: B 313 TYR cc_start: 0.8955 (m-80) cc_final: 0.8376 (m-80) REVERT: B 1050 MET cc_start: 0.8107 (ptp) cc_final: 0.7842 (ptp) REVERT: C 697 MET cc_start: 0.8790 (ppp) cc_final: 0.8400 (ppp) REVERT: E 34 MET cc_start: 0.7144 (tmm) cc_final: 0.6732 (mtp) REVERT: E 72 ILE cc_start: 0.8742 (pt) cc_final: 0.8299 (pt) REVERT: E 140 MET cc_start: 0.8713 (mmp) cc_final: 0.7872 (mmp) REVERT: E 144 PHE cc_start: 0.7868 (m-10) cc_final: 0.7253 (m-10) REVERT: D 49 ARG cc_start: 0.5781 (tpm170) cc_final: 0.5215 (tpt90) REVERT: D 140 MET cc_start: 0.5587 (ptt) cc_final: 0.3880 (mtt) REVERT: F 34 MET cc_start: 0.2419 (mpp) cc_final: 0.2177 (mpp) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.3191 time to fit residues: 92.7984 Evaluate side-chains 108 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 112 optimal weight: 8.9990 chunk 300 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 195 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 333 optimal weight: 9.9990 chunk 277 optimal weight: 6.9990 chunk 154 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26898 Z= 0.221 Angle : 0.596 11.167 36620 Z= 0.308 Chirality : 0.046 0.443 4282 Planarity : 0.004 0.054 4758 Dihedral : 6.140 55.937 4355 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.07 % Favored : 92.87 % Rotamer: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.34 % Cbeta Deviations : 0.00 % 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: -1.61 (0.14), residues: 3410 helix: 0.12 (0.16), residues: 1002 sheet: -0.67 (0.22), residues: 529 loop : -1.91 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.012 0.001 HIS E 138 PHE 0.029 0.002 PHE C 759 TYR 0.028 0.001 TYR C 873 ARG 0.008 0.000 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1005 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8447 (tm-30) REVERT: B 160 TYR cc_start: 0.7468 (p90) cc_final: 0.7222 (p90) REVERT: B 313 TYR cc_start: 0.8951 (m-80) cc_final: 0.8270 (m-80) REVERT: C 464 PHE cc_start: 0.6310 (m-10) cc_final: 0.5513 (p90) REVERT: C 697 MET cc_start: 0.8747 (ppp) cc_final: 0.8313 (ppp) REVERT: E 34 MET cc_start: 0.7090 (tmm) cc_final: 0.6693 (mtp) REVERT: E 72 ILE cc_start: 0.8734 (pt) cc_final: 0.8258 (pt) REVERT: E 91 ASN cc_start: 0.9250 (m110) cc_final: 0.9048 (m110) REVERT: E 140 MET cc_start: 0.8691 (mmp) cc_final: 0.7811 (mmp) REVERT: E 144 PHE cc_start: 0.7855 (m-10) cc_final: 0.7231 (m-10) REVERT: E 149 LEU cc_start: 0.8695 (mt) cc_final: 0.8141 (mt) REVERT: D 49 ARG cc_start: 0.5829 (tpm170) cc_final: 0.5228 (tpt90) REVERT: D 140 MET cc_start: 0.5640 (ptt) cc_final: 0.5088 (ptt) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.3450 time to fit residues: 101.6548 Evaluate side-chains 106 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 321 optimal weight: 40.0000 chunk 37 optimal weight: 20.0000 chunk 190 optimal weight: 0.8980 chunk 243 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 280 optimal weight: 8.9990 chunk 186 optimal weight: 0.8980 chunk 332 optimal weight: 5.9990 chunk 208 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26898 Z= 0.226 Angle : 0.591 10.629 36620 Z= 0.304 Chirality : 0.046 0.428 4282 Planarity : 0.004 0.055 4758 Dihedral : 5.987 55.741 4355 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.39 % Favored : 92.55 % Rotamer: Outliers : 0.04 % Allowed : 1.72 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3410 helix: 0.29 (0.17), residues: 997 sheet: -0.61 (0.22), residues: 524 loop : -1.84 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 436 HIS 0.013 0.001 HIS C1048 PHE 0.023 0.002 PHE F 144 TYR 0.015 0.001 TYR E 145 ARG 0.005 0.000 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1005 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8510 (tm-30) REVERT: B 313 TYR cc_start: 0.8940 (m-80) cc_final: 0.8233 (m-80) REVERT: B 432 CYS cc_start: 0.7605 (m) cc_final: 0.7398 (m) REVERT: B 1050 MET cc_start: 0.8283 (ptp) cc_final: 0.7384 (ptp) REVERT: C 464 PHE cc_start: 0.6226 (m-10) cc_final: 0.5435 (p90) REVERT: E 34 MET cc_start: 0.7085 (tmm) cc_final: 0.6694 (mtp) REVERT: E 72 ILE cc_start: 0.8768 (pt) cc_final: 0.8315 (pt) REVERT: E 140 MET cc_start: 0.8680 (mmp) cc_final: 0.7789 (mmp) REVERT: E 144 PHE cc_start: 0.7776 (m-10) cc_final: 0.7087 (m-10) REVERT: E 149 LEU cc_start: 0.8695 (mt) cc_final: 0.8075 (mt) REVERT: D 49 ARG cc_start: 0.5850 (tpm170) cc_final: 0.5211 (tpt90) REVERT: D 140 MET cc_start: 0.5786 (ptt) cc_final: 0.4073 (mmt) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.3355 time to fit residues: 91.6697 Evaluate side-chains 104 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 205 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 198 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 261 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26898 Z= 0.191 Angle : 0.573 9.944 36620 Z= 0.295 Chirality : 0.046 0.429 4282 Planarity : 0.004 0.056 4758 Dihedral : 5.760 54.846 4355 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.04 % Favored : 92.90 % Rotamer: Outliers : 0.04 % Allowed : 1.29 % Favored : 98.67 % Cbeta Deviations : 0.00 % 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: -1.34 (0.14), residues: 3410 helix: 0.41 (0.17), residues: 1003 sheet: -0.52 (0.22), residues: 522 loop : -1.78 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 436 HIS 0.011 0.001 HIS E 138 PHE 0.020 0.001 PHE F 144 TYR 0.036 0.001 TYR C 873 ARG 0.004 0.000 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1005 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8481 (tm-30) REVERT: B 313 TYR cc_start: 0.8892 (m-80) cc_final: 0.8199 (m-80) REVERT: C 464 PHE cc_start: 0.6111 (m-10) cc_final: 0.5334 (p90) REVERT: C 1050 MET cc_start: 0.8387 (ptp) cc_final: 0.8140 (ptp) REVERT: E 34 MET cc_start: 0.7094 (tmm) cc_final: 0.6696 (mtp) REVERT: E 72 ILE cc_start: 0.8796 (pt) cc_final: 0.8340 (pt) REVERT: E 140 MET cc_start: 0.8684 (mmp) cc_final: 0.7784 (mmp) REVERT: E 144 PHE cc_start: 0.7820 (m-10) cc_final: 0.7192 (m-10) REVERT: E 149 LEU cc_start: 0.8687 (mt) cc_final: 0.8134 (mt) REVERT: D 49 ARG cc_start: 0.5853 (tpm170) cc_final: 0.5193 (tpt90) REVERT: D 55 SER cc_start: 0.6897 (t) cc_final: 0.6291 (t) REVERT: D 140 MET cc_start: 0.5927 (ptt) cc_final: 0.4326 (mmm) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.3584 time to fit residues: 100.5585 Evaluate side-chains 110 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 302 optimal weight: 20.0000 chunk 318 optimal weight: 30.0000 chunk 290 optimal weight: 6.9990 chunk 309 optimal weight: 9.9990 chunk 186 optimal weight: 8.9990 chunk 134 optimal weight: 0.5980 chunk 243 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 280 optimal weight: 8.9990 chunk 293 optimal weight: 0.6980 chunk 308 optimal weight: 6.9990 overall best weight: 4.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN E 146 GLN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 26898 Z= 0.368 Angle : 0.684 10.469 36620 Z= 0.352 Chirality : 0.048 0.437 4282 Planarity : 0.004 0.056 4758 Dihedral : 6.312 59.036 4355 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.86 % Favored : 91.09 % Rotamer: Outliers : 0.08 % Allowed : 0.98 % Favored : 98.94 % Cbeta Deviations : 0.00 % 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: -1.54 (0.14), residues: 3410 helix: 0.28 (0.17), residues: 996 sheet: -0.74 (0.22), residues: 546 loop : -1.90 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 436 HIS 0.015 0.002 HIS C1048 PHE 0.039 0.002 PHE F 144 TYR 0.019 0.002 TYR A1007 ARG 0.007 0.001 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 2.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1005 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8650 (tm-30) REVERT: B 313 TYR cc_start: 0.8980 (m-80) cc_final: 0.8371 (m-80) REVERT: C 464 PHE cc_start: 0.6296 (m-10) cc_final: 0.5483 (p90) REVERT: C 1050 MET cc_start: 0.8539 (ptp) cc_final: 0.8241 (ptp) REVERT: E 34 MET cc_start: 0.7184 (tmm) cc_final: 0.6722 (mtp) REVERT: E 72 ILE cc_start: 0.8795 (pt) cc_final: 0.8412 (pt) REVERT: E 140 MET cc_start: 0.8682 (mmp) cc_final: 0.7798 (mmp) REVERT: E 144 PHE cc_start: 0.7755 (m-10) cc_final: 0.7085 (m-10) REVERT: E 149 LEU cc_start: 0.8721 (mt) cc_final: 0.8086 (mt) REVERT: D 49 ARG cc_start: 0.5911 (tpm170) cc_final: 0.5228 (tpt90) REVERT: D 140 MET cc_start: 0.5828 (ptt) cc_final: 0.5465 (ptt) outliers start: 2 outliers final: 0 residues processed: 155 average time/residue: 0.3352 time to fit residues: 88.6026 Evaluate side-chains 106 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 203 optimal weight: 9.9990 chunk 327 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 227 optimal weight: 10.0000 chunk 343 optimal weight: 10.0000 chunk 316 optimal weight: 30.0000 chunk 273 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26898 Z= 0.264 Angle : 0.616 10.630 36620 Z= 0.317 Chirality : 0.047 0.425 4282 Planarity : 0.004 0.055 4758 Dihedral : 6.144 55.641 4355 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.77 % Favored : 92.17 % Rotamer: Outliers : 0.08 % Allowed : 0.67 % Favored : 99.26 % Cbeta Deviations : 0.00 % 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 (0.14), residues: 3410 helix: 0.33 (0.17), residues: 1000 sheet: -0.62 (0.22), residues: 548 loop : -1.87 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 104 HIS 0.013 0.001 HIS E 138 PHE 0.019 0.002 PHE F 144 TYR 0.015 0.001 TYR C 873 ARG 0.006 0.000 ARG D 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9258 (pmm) cc_final: 0.8943 (pmm) REVERT: A 1005 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8655 (tm-30) REVERT: B 313 TYR cc_start: 0.8898 (m-80) cc_final: 0.8272 (m-80) REVERT: B 432 CYS cc_start: 0.7815 (m) cc_final: 0.7591 (m) REVERT: C 464 PHE cc_start: 0.6190 (m-10) cc_final: 0.5385 (p90) REVERT: C 697 MET cc_start: 0.8933 (ppp) cc_final: 0.8203 (ppp) REVERT: E 34 MET cc_start: 0.7133 (tmm) cc_final: 0.6667 (mtp) REVERT: E 72 ILE cc_start: 0.8825 (pt) cc_final: 0.8445 (pt) REVERT: E 140 MET cc_start: 0.8679 (mmp) cc_final: 0.7819 (mmp) REVERT: E 144 PHE cc_start: 0.7880 (m-10) cc_final: 0.7179 (m-10) REVERT: E 149 LEU cc_start: 0.8705 (mt) cc_final: 0.8045 (mt) REVERT: D 49 ARG cc_start: 0.5926 (tpm170) cc_final: 0.5205 (tpt90) REVERT: D 126 LEU cc_start: 0.6819 (pp) cc_final: 0.6615 (pp) REVERT: D 140 MET cc_start: 0.5951 (ptt) cc_final: 0.4241 (mmt) outliers start: 2 outliers final: 0 residues processed: 150 average time/residue: 0.3453 time to fit residues: 89.1568 Evaluate side-chains 106 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 217 optimal weight: 9.9990 chunk 291 optimal weight: 0.0020 chunk 83 optimal weight: 0.1980 chunk 252 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 76 optimal weight: 0.7980 chunk 274 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 281 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A1010 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.076199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054705 restraints weight = 147280.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.056137 restraints weight = 73843.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.057103 restraints weight = 45479.298| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26898 Z= 0.176 Angle : 0.574 10.053 36620 Z= 0.293 Chirality : 0.046 0.416 4282 Planarity : 0.004 0.055 4758 Dihedral : 5.682 53.848 4355 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.72 % Favored : 93.23 % Rotamer: Outliers : 0.08 % Allowed : 0.20 % Favored : 99.73 % Cbeta Deviations : 0.00 % 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: -1.27 (0.14), residues: 3410 helix: 0.47 (0.17), residues: 1001 sheet: -0.52 (0.22), residues: 563 loop : -1.75 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 104 HIS 0.013 0.001 HIS E 138 PHE 0.023 0.001 PHE C 759 TYR 0.014 0.001 TYR C 265 ARG 0.004 0.000 ARG D 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4002.77 seconds wall clock time: 75 minutes 26.36 seconds (4526.36 seconds total)