Starting phenix.real_space_refine (version: 1.21rc1) on Mon Aug 21 13:22:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dm1_7961/08_2023/6dm1_7961_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dm1_7961/08_2023/6dm1_7961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dm1_7961/08_2023/6dm1_7961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dm1_7961/08_2023/6dm1_7961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dm1_7961/08_2023/6dm1_7961_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dm1_7961/08_2023/6dm1_7961_neut_trim_updated.pdb" } resolution = 4.2 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 172 5.16 5 Cl 4 4.86 5 C 20018 2.51 5 N 5133 2.21 5 O 5770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 68": "NH1" <-> "NH2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 1005": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "A PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1203": "NH1" <-> "NH2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 1005": "NH1" <-> "NH2" Residue "B TYR 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1036": "NH1" <-> "NH2" Residue "B PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1203": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C ARG 309": "NH1" <-> "NH2" Residue "C ARG 331": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 1005": "NH1" <-> "NH2" Residue "C ARG 1036": "NH1" <-> "NH2" Residue "C PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1203": "NH1" <-> "NH2" Residue "D PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 331": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Residue "D ARG 1005": "NH1" <-> "NH2" Residue "D TYR 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1036": "NH1" <-> "NH2" Residue "D PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1203": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 31097 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7730 Classifications: {'peptide': 983} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 957} Chain breaks: 4 Chain: "B" Number of atoms: 7735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7735 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 21, 'TRANS': 958} Chain breaks: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7734 Classifications: {'peptide': 984} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 958} Chain breaks: 4 Chain: "D" Number of atoms: 7735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7735 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 21, 'TRANS': 958} Chain breaks: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'CYZ': 1, 'GYY': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Time building chain proxies: 15.15, per 1000 atoms: 0.49 Number of scatterers: 31097 At special positions: 0 Unit cell: (115.56, 167.4, 199.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 172 16.00 O 5770 8.00 N 5133 7.00 C 20018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.02 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.03 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.96 Conformation dependent library (CDL) restraints added in 4.8 seconds 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 133 helices and 32 sheets defined 42.9% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.45 Creating SS restraints... Processing helix chain 'A' and resid 23 through 36 Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.691A pdb=" N THR A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.585A pdb=" N LEU A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 198 through 211 removed outlier: 3.940A pdb=" N ASP A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 280 through 301 removed outlier: 3.674A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 334 Processing helix chain 'A' and resid 417 through 420 removed outlier: 3.542A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 424 through 436 removed outlier: 3.502A pdb=" N LEU A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 523 through 544 removed outlier: 3.527A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.784A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 623 removed outlier: 4.325A pdb=" N VAL A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 612 " --> pdb=" O PHE A 608 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 641 removed outlier: 4.219A pdb=" N GLU A 637 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASP A 638 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 755 removed outlier: 3.922A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 793 through 819 removed outlier: 3.641A pdb=" N ILE A 798 " --> pdb=" O GLY A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1027 Processing helix chain 'A' and resid 1092 through 1094 No H-bonds generated for 'chain 'A' and resid 1092 through 1094' Processing helix chain 'A' and resid 1096 through 1101 Processing helix chain 'A' and resid 1106 through 1124 removed outlier: 3.805A pdb=" N SER A1110 " --> pdb=" O PHE A1106 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A1111 " --> pdb=" O PRO A1107 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A1112 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A1120 " --> pdb=" O MET A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1159 removed outlier: 3.563A pdb=" N ALA A1137 " --> pdb=" O ILE A1133 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A1138 " --> pdb=" O ILE A1134 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A1139 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A1141 " --> pdb=" O ALA A1137 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A1145 " --> pdb=" O PHE A1141 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A1150 " --> pdb=" O LEU A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1206 removed outlier: 3.970A pdb=" N VAL A1194 " --> pdb=" O MET A1191 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A1196 " --> pdb=" O GLY A1193 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP A1202 " --> pdb=" O MET A1199 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS A1204 " --> pdb=" O ILE A1201 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A1206 " --> pdb=" O ARG A1203 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.902A pdb=" N VAL B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.712A pdb=" N THR B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 144 through 155 removed outlier: 3.585A pdb=" N LEU B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 198 through 211 removed outlier: 3.829A pdb=" N ASP B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 280 through 301 removed outlier: 3.614A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.843A pdb=" N GLN B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.576A pdb=" N GLU B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 520 Proline residue: B 520 - end of helix No H-bonds generated for 'chain 'B' and resid 517 through 520' Processing helix chain 'B' and resid 523 through 543 Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.768A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 618 removed outlier: 4.483A pdb=" N VAL B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 615 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 623 Processing helix chain 'B' and resid 638 through 641 No H-bonds generated for 'chain 'B' and resid 638 through 641' Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.547A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 743 through 755 removed outlier: 4.130A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 774 through 780 removed outlier: 3.846A pdb=" N SER B 778 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY B 779 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER B 780 " --> pdb=" O ASP B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 818 Processing helix chain 'B' and resid 1008 through 1027 removed outlier: 3.628A pdb=" N LEU B1022 " --> pdb=" O ALA B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1088 No H-bonds generated for 'chain 'B' and resid 1086 through 1088' Processing helix chain 'B' and resid 1092 through 1102 Processing helix chain 'B' and resid 1105 through 1122 Processing helix chain 'B' and resid 1133 through 1159 removed outlier: 4.161A pdb=" N GLY B1138 " --> pdb=" O ILE B1134 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE B1139 " --> pdb=" O LEU B1135 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B1140 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B1141 " --> pdb=" O ALA B1137 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B1154 " --> pdb=" O ILE B1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1208 removed outlier: 3.784A pdb=" N LEU B1195 " --> pdb=" O MET B1191 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B1197 " --> pdb=" O GLY B1193 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS B1198 " --> pdb=" O VAL B1194 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 36 Processing helix chain 'C' and resid 55 through 68 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.694A pdb=" N THR C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 144 through 155 removed outlier: 3.581A pdb=" N LEU C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 198 through 211 removed outlier: 3.944A pdb=" N ASP C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 280 through 301 removed outlier: 3.674A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG C 300 " --> pdb=" O PHE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 334 Processing helix chain 'C' and resid 417 through 420 removed outlier: 3.557A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 424 through 436 removed outlier: 3.838A pdb=" N ALA C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 468 Processing helix chain 'C' and resid 523 through 544 removed outlier: 3.516A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 removed outlier: 3.788A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 623 removed outlier: 4.322A pdb=" N VAL C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 610 " --> pdb=" O TRP C 606 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 612 " --> pdb=" O PHE C 608 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 641 removed outlier: 4.198A pdb=" N GLU C 637 " --> pdb=" O GLU C 634 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASP C 638 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 696 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 755 removed outlier: 3.955A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS C 752 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 753 " --> pdb=" O ALA C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 767 Processing helix chain 'C' and resid 789 through 791 No H-bonds generated for 'chain 'C' and resid 789 through 791' Processing helix chain 'C' and resid 793 through 819 removed outlier: 3.636A pdb=" N ILE C 798 " --> pdb=" O GLY C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1027 Processing helix chain 'C' and resid 1092 through 1094 No H-bonds generated for 'chain 'C' and resid 1092 through 1094' Processing helix chain 'C' and resid 1096 through 1101 Processing helix chain 'C' and resid 1106 through 1124 removed outlier: 3.793A pdb=" N SER C1110 " --> pdb=" O PHE C1106 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C1111 " --> pdb=" O PRO C1107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C1112 " --> pdb=" O ILE C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1133 through 1159 removed outlier: 3.563A pdb=" N ALA C1137 " --> pdb=" O ILE C1133 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C1138 " --> pdb=" O ILE C1134 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE C1139 " --> pdb=" O LEU C1135 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE C1141 " --> pdb=" O ALA C1137 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY C1145 " --> pdb=" O PHE C1141 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C1150 " --> pdb=" O LEU C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1208 removed outlier: 3.968A pdb=" N VAL C1194 " --> pdb=" O MET C1191 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C1196 " --> pdb=" O GLY C1193 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP C1202 " --> pdb=" O MET C1199 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS C1204 " --> pdb=" O ILE C1201 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN C1206 " --> pdb=" O ARG C1203 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 removed outlier: 3.907A pdb=" N VAL D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.711A pdb=" N THR D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 144 through 155 removed outlier: 3.583A pdb=" N LEU D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 198 through 211 removed outlier: 3.819A pdb=" N ASP D 206 " --> pdb=" O ASN D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 263 Processing helix chain 'D' and resid 280 through 301 removed outlier: 3.601A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 removed outlier: 3.834A pdb=" N GLN D 335 " --> pdb=" O ARG D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 462 through 468 removed outlier: 3.552A pdb=" N GLU D 466 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 543 Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.768A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 618 removed outlier: 4.486A pdb=" N VAL D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 615 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 623 Processing helix chain 'D' and resid 638 through 641 No H-bonds generated for 'chain 'D' and resid 638 through 641' Processing helix chain 'D' and resid 654 through 661 removed outlier: 3.539A pdb=" N ARG D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 743 through 755 removed outlier: 4.110A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS D 752 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 774 through 780 removed outlier: 3.842A pdb=" N SER D 778 " --> pdb=" O ALA D 775 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY D 779 " --> pdb=" O LYS D 776 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER D 780 " --> pdb=" O ASP D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 818 Processing helix chain 'D' and resid 1008 through 1027 removed outlier: 3.630A pdb=" N LEU D1022 " --> pdb=" O ALA D1018 " (cutoff:3.500A) Processing helix chain 'D' and resid 1086 through 1088 No H-bonds generated for 'chain 'D' and resid 1086 through 1088' Processing helix chain 'D' and resid 1092 through 1102 Processing helix chain 'D' and resid 1105 through 1122 Processing helix chain 'D' and resid 1133 through 1159 removed outlier: 4.165A pdb=" N GLY D1138 " --> pdb=" O ILE D1134 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE D1139 " --> pdb=" O LEU D1135 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE D1141 " --> pdb=" O ALA D1137 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D1154 " --> pdb=" O ILE D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1177 through 1208 removed outlier: 3.792A pdb=" N LEU D1195 " --> pdb=" O MET D1191 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D1197 " --> pdb=" O GLY D1193 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS D1198 " --> pdb=" O VAL D1194 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 42 through 49 Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 159 through 164 removed outlier: 5.101A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N HIS A 219 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU A 194 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU A 241 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE A 222 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER A 243 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 394 through 399 removed outlier: 7.004A pdb=" N LYS A 439 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL A 397 " --> pdb=" O LYS A 439 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LYS A 441 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR A 399 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N THR A 443 " --> pdb=" O THR A 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= F, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.955A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 498 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 720 through 723 removed outlier: 4.419A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1033 through 1036 removed outlier: 3.582A pdb=" N SER A1035 " --> pdb=" O THR A1058 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 43 through 49 removed outlier: 6.496A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N HIS B 46 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ASP B 48 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 72 " --> pdb=" O GLY B 15 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU B 17 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE B 74 " --> pdb=" O LEU B 17 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= K, first strand: chain 'B' and resid 159 through 164 removed outlier: 5.251A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS B 219 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU B 194 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU B 241 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE B 222 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER B 243 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= M, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= N, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.954A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.425A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 1033 through 1036 removed outlier: 3.598A pdb=" N SER B1035 " --> pdb=" O THR B1058 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 42 through 49 Processing sheet with id= R, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= S, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.100A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS C 219 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU C 194 " --> pdb=" O HIS C 219 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU C 241 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE C 222 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER C 243 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 394 through 399 removed outlier: 6.996A pdb=" N LYS C 439 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL C 397 " --> pdb=" O LYS C 439 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS C 441 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR C 399 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR C 443 " --> pdb=" O THR C 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= V, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.946A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 720 through 723 removed outlier: 4.421A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 1033 through 1036 removed outlier: 3.575A pdb=" N SER C1035 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS C1066 " --> pdb=" O HIS C1059 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 43 through 49 removed outlier: 6.491A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N HIS D 46 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA D 72 " --> pdb=" O GLY D 15 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N LEU D 17 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE D 74 " --> pdb=" O LEU D 17 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'D' and resid 96 through 98 Processing sheet with id= AA, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.248A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS D 219 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU D 194 " --> pdb=" O HIS D 219 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE D 221 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLU D 241 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE D 222 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER D 243 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= AC, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= AD, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.981A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.431A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 1033 through 1036 removed outlier: 3.602A pdb=" N SER D1035 " --> pdb=" O THR D1058 " (cutoff:3.500A) 1196 hydrogen bonds defined for protein. 3396 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: 11.51 Time building geometry restraints manager: 12.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 545 1.23 - 1.38: 11831 1.38 - 1.53: 18315 1.53 - 1.69: 799 1.69 - 1.84: 280 Bond restraints: 31770 Sorted by residual: bond pdb=" C4 CYZ B1302 " pdb=" C5 CYZ B1302 " ideal model delta sigma weight residual 1.512 1.079 0.433 2.00e-02 2.50e+03 4.68e+02 bond pdb=" C4 CYZ D1302 " pdb=" C5 CYZ D1302 " ideal model delta sigma weight residual 1.512 1.080 0.432 2.00e-02 2.50e+03 4.67e+02 bond pdb=" C4 CYZ C1302 " pdb=" C5 CYZ C1302 " ideal model delta sigma weight residual 1.512 1.080 0.432 2.00e-02 2.50e+03 4.66e+02 bond pdb=" C4 CYZ A1302 " pdb=" C5 CYZ A1302 " ideal model delta sigma weight residual 1.512 1.081 0.431 2.00e-02 2.50e+03 4.64e+02 bond pdb=" C1 CYZ C1302 " pdb=" C2 CYZ C1302 " ideal model delta sigma weight residual 1.557 1.126 0.431 2.00e-02 2.50e+03 4.64e+02 ... (remaining 31765 not shown) Histogram of bond angle deviations from ideal: 87.27 - 97.39: 20 97.39 - 107.50: 1005 107.50 - 117.62: 22141 117.62 - 127.73: 19514 127.73 - 137.85: 252 Bond angle restraints: 42932 Sorted by residual: angle pdb=" C1 CYZ D1302 " pdb=" C2 CYZ D1302 " pdb=" C3 CYZ D1302 " ideal model delta sigma weight residual 106.92 137.85 -30.93 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C1 CYZ B1302 " pdb=" C2 CYZ B1302 " pdb=" C3 CYZ B1302 " ideal model delta sigma weight residual 106.92 137.77 -30.85 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C1 CYZ C1302 " pdb=" C2 CYZ C1302 " pdb=" C3 CYZ C1302 " ideal model delta sigma weight residual 106.92 137.71 -30.79 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C1 CYZ A1302 " pdb=" C2 CYZ A1302 " pdb=" C3 CYZ A1302 " ideal model delta sigma weight residual 106.92 137.66 -30.74 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C4 CYZ C1302 " pdb=" C5 CYZ C1302 " pdb=" C6 CYZ C1302 " ideal model delta sigma weight residual 105.93 132.25 -26.32 3.00e+00 1.11e-01 7.70e+01 ... (remaining 42927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.45: 18010 19.45 - 38.90: 635 38.90 - 58.35: 66 58.35 - 77.80: 17 77.80 - 97.25: 5 Dihedral angle restraints: 18733 sinusoidal: 7412 harmonic: 11321 Sorted by residual: dihedral pdb=" CA SER D 635 " pdb=" C SER D 635 " pdb=" N ALA D 636 " pdb=" CA ALA D 636 " ideal model delta harmonic sigma weight residual -180.00 -124.97 -55.03 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA SER B 635 " pdb=" C SER B 635 " pdb=" N ALA B 636 " pdb=" CA ALA B 636 " ideal model delta harmonic sigma weight residual -180.00 -125.17 -54.83 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CA PRO C 632 " pdb=" C PRO C 632 " pdb=" N ILE C 633 " pdb=" CA ILE C 633 " ideal model delta harmonic sigma weight residual -180.00 -135.68 -44.32 0 5.00e+00 4.00e-02 7.86e+01 ... (remaining 18730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.436: 4748 0.436 - 0.872: 6 0.872 - 1.308: 0 1.308 - 1.744: 0 1.744 - 2.180: 8 Chirality restraints: 4762 Sorted by residual: chirality pdb=" C5 CYZ B1302 " pdb=" C4 CYZ B1302 " pdb=" C6 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 1.13 2.18 2.00e-01 2.50e+01 1.19e+02 chirality pdb=" C5 CYZ D1302 " pdb=" C4 CYZ D1302 " pdb=" C6 CYZ D1302 " pdb=" C7 CYZ D1302 " both_signs ideal model delta sigma weight residual False 3.31 1.13 2.18 2.00e-01 2.50e+01 1.19e+02 chirality pdb=" C5 CYZ C1302 " pdb=" C4 CYZ C1302 " pdb=" C6 CYZ C1302 " pdb=" C7 CYZ C1302 " both_signs ideal model delta sigma weight residual False 3.31 1.13 2.18 2.00e-01 2.50e+01 1.18e+02 ... (remaining 4759 not shown) Planarity restraints: 5385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 98 " -0.061 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO C 99 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 98 " 0.061 5.00e-02 4.00e+02 9.25e-02 1.37e+01 pdb=" N PRO A 99 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " -0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO B 99 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.043 5.00e-02 4.00e+02 ... (remaining 5382 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1659 2.72 - 3.26: 30784 3.26 - 3.81: 49914 3.81 - 4.35: 57513 4.35 - 4.90: 96586 Nonbonded interactions: 236456 Sorted by model distance: nonbonded pdb=" O ILE C1025 " pdb=" OG1 THR C1029 " model vdw 2.171 2.440 nonbonded pdb=" O ILE A1025 " pdb=" OG1 THR A1029 " model vdw 2.212 2.440 nonbonded pdb=" O ALA D1026 " pdb=" OG SER D1178 " model vdw 2.227 2.440 nonbonded pdb=" O ALA B1026 " pdb=" OG SER B1178 " model vdw 2.231 2.440 nonbonded pdb=" O GLU B 637 " pdb=" OG SER B 640 " model vdw 2.236 2.440 ... (remaining 236451 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 10 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 817 or (resid 818 and \ (name N or name CA or name C or name O or name CB )) or resid 819 or resid 1002 \ through 1208 or resid 1301 through 1302)) selection = (chain 'B' and (resid 10 through 549 or resid 565 through 1208 or resid 1301 thr \ ough 1302)) selection = (chain 'C' and (resid 10 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 817 or (resid 818 and \ (name N or name CA or name C or name O or name CB )) or resid 819 or resid 1002 \ through 1208 or resid 1301 through 1302)) selection = (chain 'D' and (resid 10 through 549 or resid 565 through 1208 or resid 1301 thr \ ough 1302)) } 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.480 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 78.290 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.433 31770 Z= 0.837 Angle : 1.192 30.927 42932 Z= 0.642 Chirality : 0.104 2.180 4762 Planarity : 0.007 0.093 5385 Dihedral : 10.331 97.247 11457 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.42 % Favored : 91.17 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.78 (0.11), residues: 3897 helix: -1.99 (0.09), residues: 1788 sheet: -2.05 (0.24), residues: 410 loop : -3.17 (0.12), residues: 1699 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 796 time to evaluate : 3.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 0 residues processed: 806 average time/residue: 0.4576 time to fit residues: 576.2302 Evaluate side-chains 363 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 3.664 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 6.9990 chunk 297 optimal weight: 30.0000 chunk 164 optimal weight: 0.0980 chunk 101 optimal weight: 0.9990 chunk 200 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 307 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 355 optimal weight: 8.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 147 GLN A 207 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 435 HIS A 642 GLN A1198 HIS B 24 GLN B 147 GLN B 246 GLN B 355 ASN B 412 HIS B 642 GLN B 764 ASN C 46 HIS C 147 GLN C 207 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS C 435 HIS C1198 HIS D 24 GLN D 246 GLN D 355 ASN D 412 HIS D 435 HIS D 642 GLN D 764 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 31770 Z= 0.311 Angle : 0.705 12.413 42932 Z= 0.372 Chirality : 0.044 0.276 4762 Planarity : 0.005 0.074 5385 Dihedral : 6.537 97.945 4295 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.11 % Favored : 92.56 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.94 (0.12), residues: 3897 helix: 0.23 (0.12), residues: 1744 sheet: -1.66 (0.25), residues: 406 loop : -2.86 (0.12), residues: 1747 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 396 time to evaluate : 3.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 397 average time/residue: 0.4272 time to fit residues: 277.7224 Evaluate side-chains 243 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 3.830 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 242 optimal weight: 0.0980 chunk 98 optimal weight: 10.0000 chunk 356 optimal weight: 10.0000 chunk 385 optimal weight: 10.0000 chunk 317 optimal weight: 4.9990 chunk 353 optimal weight: 0.5980 chunk 121 optimal weight: 0.1980 chunk 286 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN B 642 GLN B1159 ASN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN D 642 GLN D1159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 31770 Z= 0.189 Angle : 0.580 9.546 42932 Z= 0.304 Chirality : 0.041 0.233 4762 Planarity : 0.004 0.065 5385 Dihedral : 5.898 89.414 4295 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.47 % Favored : 93.35 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 3897 helix: 0.98 (0.12), residues: 1763 sheet: -1.29 (0.26), residues: 404 loop : -2.65 (0.13), residues: 1730 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 341 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 343 average time/residue: 0.4029 time to fit residues: 228.2830 Evaluate side-chains 239 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 3.308 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 0.9990 chunk 268 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 357 optimal weight: 6.9990 chunk 378 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 339 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN A 642 GLN A1059 HIS B 219 HIS B 246 GLN B 355 ASN B 642 GLN C 147 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN C 642 GLN C1059 HIS D 219 HIS D 246 GLN D 355 ASN D 642 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 31770 Z= 0.268 Angle : 0.631 8.830 42932 Z= 0.330 Chirality : 0.042 0.246 4762 Planarity : 0.004 0.069 5385 Dihedral : 6.077 97.333 4295 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.80 % Favored : 91.99 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 3897 helix: 1.22 (0.13), residues: 1749 sheet: -1.24 (0.26), residues: 386 loop : -2.47 (0.13), residues: 1762 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 301 time to evaluate : 3.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.3794 time to fit residues: 194.9755 Evaluate side-chains 225 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 3.490 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 282 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 chunk 323 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 193 optimal weight: 9.9990 chunk 340 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN B 355 ASN C 147 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 31770 Z= 0.241 Angle : 0.605 12.698 42932 Z= 0.314 Chirality : 0.041 0.243 4762 Planarity : 0.004 0.059 5385 Dihedral : 5.945 95.657 4295 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.21 % Favored : 92.64 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.13), residues: 3897 helix: 1.29 (0.12), residues: 1757 sheet: -1.31 (0.25), residues: 433 loop : -2.38 (0.14), residues: 1707 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 298 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 300 average time/residue: 0.3933 time to fit residues: 199.3228 Evaluate side-chains 214 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 3.811 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 3.9990 chunk 341 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 chunk 222 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 379 optimal weight: 1.9990 chunk 314 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 246 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN B 355 ASN C 24 GLN C 246 GLN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 31770 Z= 0.164 Angle : 0.560 11.851 42932 Z= 0.290 Chirality : 0.040 0.225 4762 Planarity : 0.004 0.088 5385 Dihedral : 5.631 92.781 4295 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.83 % Favored : 93.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3897 helix: 1.56 (0.13), residues: 1744 sheet: -1.28 (0.25), residues: 445 loop : -2.24 (0.14), residues: 1708 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 3.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.3881 time to fit residues: 193.1388 Evaluate side-chains 221 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 3.793 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 276 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 319 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 377 optimal weight: 0.8980 chunk 236 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 174 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN B 355 ASN B 764 ASN D 764 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 31770 Z= 0.177 Angle : 0.562 11.361 42932 Z= 0.290 Chirality : 0.040 0.222 4762 Planarity : 0.004 0.091 5385 Dihedral : 5.551 93.339 4295 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.59 % Favored : 93.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3897 helix: 1.64 (0.13), residues: 1742 sheet: -1.23 (0.25), residues: 427 loop : -2.18 (0.14), residues: 1728 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.3707 time to fit residues: 184.4776 Evaluate side-chains 223 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 3.835 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 240 optimal weight: 0.5980 chunk 257 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 296 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN A 642 GLN B 355 ASN C 575 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 31770 Z= 0.163 Angle : 0.558 11.195 42932 Z= 0.288 Chirality : 0.040 0.228 4762 Planarity : 0.004 0.080 5385 Dihedral : 5.463 92.838 4295 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.52 % Favored : 93.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3897 helix: 1.62 (0.13), residues: 1756 sheet: -1.29 (0.25), residues: 437 loop : -2.14 (0.14), residues: 1704 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 3.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.3912 time to fit residues: 197.3638 Evaluate side-chains 231 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 3.925 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 10.0000 chunk 361 optimal weight: 0.5980 chunk 330 optimal weight: 6.9990 chunk 352 optimal weight: 0.5980 chunk 211 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 276 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 chunk 332 optimal weight: 8.9990 chunk 350 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN B 355 ASN B 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.6464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 31770 Z= 0.161 Angle : 0.566 12.695 42932 Z= 0.290 Chirality : 0.040 0.229 4762 Planarity : 0.004 0.074 5385 Dihedral : 5.414 92.550 4295 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.21 % Favored : 93.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3897 helix: 1.59 (0.13), residues: 1762 sheet: -1.11 (0.25), residues: 417 loop : -2.06 (0.14), residues: 1718 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 3.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.3927 time to fit residues: 191.6536 Evaluate side-chains 228 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 3.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 0.3980 chunk 372 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 258 optimal weight: 8.9990 chunk 390 optimal weight: 0.8980 chunk 359 optimal weight: 0.0370 chunk 310 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN B 355 ASN B 435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.6585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 31770 Z= 0.138 Angle : 0.550 12.874 42932 Z= 0.281 Chirality : 0.040 0.218 4762 Planarity : 0.004 0.071 5385 Dihedral : 5.210 90.029 4295 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.42 % Favored : 93.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3897 helix: 1.67 (0.13), residues: 1771 sheet: -1.07 (0.26), residues: 423 loop : -1.98 (0.14), residues: 1703 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 3.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.3760 time to fit residues: 194.2998 Evaluate side-chains 223 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 4.037 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 0.6980 chunk 331 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 286 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 86 optimal weight: 0.2980 chunk 311 optimal weight: 0.2980 chunk 130 optimal weight: 5.9990 chunk 319 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.075623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.057969 restraints weight = 149059.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059556 restraints weight = 92203.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060616 restraints weight = 67489.300| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.6759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 31770 Z= 0.210 Angle : 0.590 12.727 42932 Z= 0.302 Chirality : 0.041 0.220 4762 Planarity : 0.004 0.072 5385 Dihedral : 5.441 95.427 4295 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.08 % Favored : 92.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3897 helix: 1.65 (0.12), residues: 1762 sheet: -1.29 (0.25), residues: 439 loop : -1.99 (0.14), residues: 1696 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5520.07 seconds wall clock time: 102 minutes 17.19 seconds (6137.19 seconds total)