Starting phenix.real_space_refine (version: 1.21rc1) on Mon Aug 21 13:29:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dm0_7960/08_2023/6dm0_7960_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dm0_7960/08_2023/6dm0_7960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dm0_7960/08_2023/6dm0_7960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dm0_7960/08_2023/6dm0_7960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dm0_7960/08_2023/6dm0_7960_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dm0_7960/08_2023/6dm0_7960_updated.pdb" } resolution = 4.4 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 20017 2.51 5 N 5132 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 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 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 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 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 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 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 31095 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" 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: "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: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {'CYZ': 1, 'GZD': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "C" 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: "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: 15.63, per 1000 atoms: 0.50 Number of scatterers: 31095 At special positions: 0 Unit cell: (115.56, 167.4, 198.72, 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 5132 7.00 C 20017 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=2.04 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.04 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=2.04 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: 12.33 Conformation dependent library (CDL) restraints added in 4.5 seconds 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 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: 136 helices and 30 sheets defined 43.3% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.54 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: 3.603A 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: 3.595A pdb=" N LEU A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.676A 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: 3.797A pdb=" N ASP A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 3.740A 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: 3.667A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.537A 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: 3.517A 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: 3.614A pdb=" N LEU A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 523 through 544 removed outlier: 3.664A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.598A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 623 removed outlier: 4.199A pdb=" N VAL A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 612 " --> pdb=" O PHE A 608 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 641 removed outlier: 4.272A pdb=" N GLU A 637 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 5.376A 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: 3.876A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.506A 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: 3.539A 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 1122 removed outlier: 3.839A pdb=" N SER A1110 " --> pdb=" O PHE A1106 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL A1111 " --> pdb=" O PRO A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1159 removed outlier: 3.582A pdb=" N ALA A1137 " --> pdb=" O ILE A1133 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY A1138 " --> pdb=" O ILE A1134 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A1139 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A1141 " --> pdb=" O ALA A1137 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A1145 " --> pdb=" O PHE A1141 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A1150 " --> pdb=" O LEU A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1208 removed outlier: 3.873A pdb=" N VAL A1194 " --> pdb=" O MET A1191 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A1196 " --> pdb=" O GLY A1193 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A1202 " --> pdb=" O MET A1199 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS A1204 " --> pdb=" O ILE A1201 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.961A 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: 3.625A 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: 3.834A pdb=" N ASP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 198 through 211 removed outlier: 3.677A 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: 3.679A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.807A 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: 3.727A pdb=" N GLU B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 520 No H-bonds generated for 'chain 'B' and resid 518 through 520' Processing helix chain 'B' and resid 523 through 543 Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.580A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 618 removed outlier: 4.433A pdb=" N VAL B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.840A 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 661 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 756 removed outlier: 4.154A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.590A 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: 3.787A pdb=" N SER B 778 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY B 779 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER B 780 " --> pdb=" O ASP B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 818 removed outlier: 3.578A pdb=" N SER B 818 " --> pdb=" O PHE B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1027 removed outlier: 3.578A 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 1160 removed outlier: 4.215A pdb=" N GLY B1138 " --> pdb=" O ILE B1134 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE B1139 " --> pdb=" O LEU B1135 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B1140 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B1141 " --> pdb=" O ALA B1137 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B1154 " --> pdb=" O ILE B1150 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA B1160 " --> pdb=" O ILE B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1208 removed outlier: 3.683A pdb=" N LEU B1195 " --> pdb=" O MET B1191 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B1197 " --> pdb=" O GLY B1193 " (cutoff:3.500A) removed outlier: 3.692A 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: 3.608A 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: 3.592A pdb=" N LEU C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.663A 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: 3.802A pdb=" N ASP C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) removed outlier: 3.743A 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: 3.665A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.528A 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: 3.523A 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: 3.674A pdb=" N ALA C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 523 through 544 removed outlier: 3.652A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 removed outlier: 3.608A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 623 removed outlier: 4.196A pdb=" N VAL C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 610 " --> pdb=" O TRP C 606 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 612 " --> pdb=" O PHE C 608 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 641 removed outlier: 4.246A pdb=" N GLU C 637 " --> pdb=" O GLU C 634 " (cutoff:3.500A) removed outlier: 5.384A 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: 3.897A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 752 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 3.513A 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: 3.533A 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 1122 removed outlier: 3.829A pdb=" N SER C1110 " --> pdb=" O PHE C1106 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL C1111 " --> pdb=" O PRO C1107 " (cutoff:3.500A) Processing helix chain 'C' and resid 1133 through 1159 removed outlier: 3.568A pdb=" N ALA C1137 " --> pdb=" O ILE C1133 " (cutoff:3.500A) removed outlier: 3.708A 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: 3.986A pdb=" N PHE C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C1141 " --> pdb=" O ALA C1137 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C1145 " --> pdb=" O PHE C1141 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C1150 " --> pdb=" O LEU C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1208 removed outlier: 3.874A pdb=" N VAL C1194 " --> pdb=" O MET C1191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C1196 " --> pdb=" O GLY C1193 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP C1202 " --> pdb=" O MET C1199 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS C1204 " --> pdb=" O ILE C1201 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 removed outlier: 3.964A 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: 3.625A 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: 3.586A pdb=" N LEU D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 198 through 211 removed outlier: 3.666A 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: 3.667A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 removed outlier: 3.803A 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: 3.714A pdb=" N GLU D 466 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 520 No H-bonds generated for 'chain 'D' and resid 518 through 520' Processing helix chain 'D' and resid 523 through 543 Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.580A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 618 removed outlier: 4.438A pdb=" N VAL D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) removed outlier: 3.841A 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 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 756 removed outlier: 4.123A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.785A pdb=" N SER D 778 " --> pdb=" O ALA D 775 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY D 779 " --> pdb=" O LYS D 776 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER D 780 " --> pdb=" O ASP D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 818 removed outlier: 3.572A pdb=" N SER D 818 " --> pdb=" O PHE D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 1008 through 1027 removed outlier: 3.578A 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 1160 removed outlier: 4.220A pdb=" N GLY D1138 " --> pdb=" O ILE D1134 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE D1139 " --> pdb=" O LEU D1135 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE D1141 " --> pdb=" O ALA D1137 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D1154 " --> pdb=" O ILE D1150 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA D1160 " --> pdb=" O ILE D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1177 through 1208 removed outlier: 3.687A pdb=" N LEU D1195 " --> pdb=" O MET D1191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D1197 " --> pdb=" O GLY D1193 " (cutoff:3.500A) removed outlier: 3.685A 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 removed outlier: 6.561A pdb=" N ALA A 72 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N LEU A 17 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N PHE A 74 " --> pdb=" O LEU A 17 " (cutoff:3.500A) 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: 5.183A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N HIS A 219 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU A 194 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU A 241 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE A 222 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER A 243 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.494A 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: 7.036A pdb=" N LYS A 439 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL A 397 " --> pdb=" O LYS A 439 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LYS A 441 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR A 399 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 5.925A 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 474 through 476 removed outlier: 3.645A pdb=" N ALA A 735 " --> pdb=" O ALA A 475 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.976A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 720 through 723 removed outlier: 4.366A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.159A 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: 3.687A pdb=" N SER A1035 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A1066 " --> pdb=" O HIS A1059 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 43 through 49 removed outlier: 6.456A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N HIS B 46 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ASP B 48 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA B 72 " --> pdb=" O GLY B 15 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LEU B 17 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE B 74 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 159 through 164 removed outlier: 5.312A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N HIS B 219 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU B 194 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU B 241 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE B 222 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER B 243 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= L, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= M, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.971A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.505A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 10.123A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 1033 through 1036 removed outlier: 3.542A pdb=" N SER B1035 " --> pdb=" O THR B1058 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 42 through 49 removed outlier: 6.557A pdb=" N ALA C 72 " --> pdb=" O GLY C 15 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU C 17 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N PHE C 74 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= R, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.181A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS C 219 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU C 194 " --> pdb=" O HIS C 219 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU C 241 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE C 222 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER C 243 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= T, first strand: chain 'C' and resid 474 through 476 removed outlier: 3.638A pdb=" N ALA C 735 " --> pdb=" O ALA C 475 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.963A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 720 through 723 removed outlier: 4.367A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 1033 through 1036 removed outlier: 3.689A pdb=" N SER C1035 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS C1066 " --> pdb=" O HIS C1059 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 43 through 49 removed outlier: 6.448A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N HIS D 46 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA D 72 " --> pdb=" O GLY D 15 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LEU D 17 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE D 74 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.310A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N HIS D 219 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU D 194 " --> pdb=" O HIS D 219 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE D 221 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU D 241 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE D 222 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER D 243 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= AA, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= AB, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.005A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.510A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 10.148A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 1033 through 1036 removed outlier: 3.548A pdb=" N SER D1035 " --> pdb=" O THR D1058 " (cutoff:3.500A) 1219 hydrogen bonds defined for protein. 3453 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: 10.68 Time building geometry restraints manager: 13.12 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: 422 1.23 - 1.38: 11526 1.38 - 1.53: 18294 1.53 - 1.68: 1247 1.68 - 1.83: 280 Bond restraints: 31769 Sorted by residual: bond pdb=" C4 CYZ B1302 " pdb=" C5 CYZ B1302 " ideal model delta sigma weight residual 1.512 1.080 0.432 2.00e-02 2.50e+03 4.66e+02 bond pdb=" C1 CYZ B1302 " pdb=" C2 CYZ B1302 " ideal model delta sigma weight residual 1.557 1.126 0.431 2.00e-02 2.50e+03 4.65e+02 bond pdb=" C4 CYZ D1302 " pdb=" C5 CYZ D1302 " ideal model delta sigma weight residual 1.512 1.081 0.431 2.00e-02 2.50e+03 4.65e+02 bond pdb=" C1 CYZ D1302 " pdb=" C2 CYZ D1302 " ideal model delta sigma weight residual 1.557 1.126 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 31764 not shown) Histogram of bond angle deviations from ideal: 87.45 - 97.44: 16 97.44 - 107.43: 948 107.43 - 117.41: 22057 117.41 - 127.40: 19631 127.40 - 137.39: 286 Bond angle restraints: 42938 Sorted by residual: angle pdb=" C1 CYZ A1302 " pdb=" C2 CYZ A1302 " pdb=" C3 CYZ A1302 " ideal model delta sigma weight residual 106.92 137.39 -30.47 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C1 CYZ D1302 " pdb=" C2 CYZ D1302 " pdb=" C3 CYZ D1302 " ideal model delta sigma weight residual 106.92 137.36 -30.44 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C1 CYZ B1302 " pdb=" C2 CYZ B1302 " pdb=" C3 CYZ B1302 " ideal model delta sigma weight residual 106.92 137.34 -30.42 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C1 CYZ C1302 " pdb=" C2 CYZ C1302 " pdb=" C3 CYZ C1302 " ideal model delta sigma weight residual 106.92 137.34 -30.42 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C4 CYZ C1302 " pdb=" C5 CYZ C1302 " pdb=" C6 CYZ C1302 " ideal model delta sigma weight residual 105.93 132.26 -26.33 3.00e+00 1.11e-01 7.70e+01 ... (remaining 42933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 17911 17.69 - 35.39: 671 35.39 - 53.08: 122 53.08 - 70.77: 12 70.77 - 88.47: 11 Dihedral angle restraints: 18727 sinusoidal: 7405 harmonic: 11322 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 -127.76 -52.24 0 5.00e+00 4.00e-02 1.09e+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 -127.86 -52.14 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA GLY A 313 " pdb=" C GLY A 313 " pdb=" N ASP A 314 " pdb=" CA ASP A 314 " ideal model delta harmonic sigma weight residual -180.00 -137.30 -42.70 0 5.00e+00 4.00e-02 7.29e+01 ... (remaining 18724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.436: 4750 0.436 - 0.872: 8 0.872 - 1.308: 0 1.308 - 1.744: 0 1.744 - 2.180: 8 Chirality restraints: 4766 Sorted by residual: 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 1.19e+02 chirality pdb=" C5 CYZ A1302 " pdb=" C4 CYZ A1302 " pdb=" C6 CYZ A1302 " pdb=" C7 CYZ A1302 " 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 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 1.18e+02 ... (remaining 4763 not shown) Planarity restraints: 5384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 98 " 0.062 5.00e-02 4.00e+02 9.46e-02 1.43e+01 pdb=" N PRO A 99 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 98 " -0.062 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO C 99 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " -0.057 5.00e-02 4.00e+02 8.75e-02 1.23e+01 pdb=" N PRO B 99 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.047 5.00e-02 4.00e+02 ... (remaining 5381 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1879 2.73 - 3.27: 31164 3.27 - 3.81: 50430 3.81 - 4.36: 57412 4.36 - 4.90: 96127 Nonbonded interactions: 237012 Sorted by model distance: nonbonded pdb=" O ILE C1025 " pdb=" OG1 THR C1029 " model vdw 2.183 2.440 nonbonded pdb=" O ILE B1025 " pdb=" OG1 THR B1029 " model vdw 2.194 2.440 nonbonded pdb=" O ILE D1025 " pdb=" OG1 THR D1029 " model vdw 2.194 2.440 nonbonded pdb=" O GLU D 637 " pdb=" OG SER D 640 " model vdw 2.217 2.440 nonbonded pdb=" O GLU B 637 " pdb=" OG SER B 640 " model vdw 2.217 2.440 ... (remaining 237007 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 1209 or resid 1301 through 1302)) selection = (chain 'B' and (resid 10 through 549 or resid 565 through 1209 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 1209 or resid 1301 through 1302)) selection = (chain 'D' and (resid 10 through 549 or resid 565 through 1209 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: 1.660 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: 8.410 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 76.710 Find NCS groups from input model: 2.440 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: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 0.432 31769 Z= 0.872 Angle : 1.104 30.472 42938 Z= 0.558 Chirality : 0.103 2.180 4766 Planarity : 0.007 0.095 5384 Dihedral : 10.159 88.467 11451 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.39 % Favored : 91.20 % Rotamer Outliers : 0.30 % 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: -3.36 (0.11), residues: 3898 helix: -1.43 (0.10), residues: 1784 sheet: -2.14 (0.23), residues: 432 loop : -3.13 (0.12), residues: 1682 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 807 time to evaluate : 3.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 814 average time/residue: 0.4599 time to fit residues: 582.2259 Evaluate side-chains 370 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 368 time to evaluate : 3.835 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2792 time to fit residues: 6.0766 ------------------------------------------------------------------------------- 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: 8.9990 chunk 297 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 200 optimal weight: 8.9990 chunk 158 optimal weight: 0.0070 chunk 307 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 228 optimal weight: 0.0470 chunk 355 optimal weight: 4.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN B 46 HIS ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 337 GLN B 412 HIS B 747 ASN C 246 GLN D 24 GLN D 46 HIS ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN D 412 HIS D 747 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 31769 Z= 0.158 Angle : 0.593 9.192 42938 Z= 0.315 Chirality : 0.040 0.172 4766 Planarity : 0.005 0.076 5384 Dihedral : 6.135 80.104 4289 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.34 % Favored : 94.36 % 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: -1.82 (0.13), residues: 3898 helix: 0.19 (0.12), residues: 1784 sheet: -1.74 (0.25), residues: 408 loop : -2.65 (0.13), residues: 1706 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 499 time to evaluate : 3.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 501 average time/residue: 0.4218 time to fit residues: 338.9037 Evaluate side-chains 338 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 336 time to evaluate : 3.544 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3159 time to fit residues: 5.9580 ------------------------------------------------------------------------------- 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: 10.0000 chunk 296 optimal weight: 9.9990 chunk 242 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 356 optimal weight: 8.9990 chunk 385 optimal weight: 9.9990 chunk 317 optimal weight: 6.9990 chunk 353 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 286 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 587 GLN A 642 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN B 791 ASN ** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN C 642 GLN D 224 ASN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN D 791 ASN ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.063 31769 Z= 0.420 Angle : 0.837 10.954 42938 Z= 0.444 Chirality : 0.046 0.235 4766 Planarity : 0.006 0.070 5384 Dihedral : 6.782 93.164 4289 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.85 % Favored : 90.82 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.73 (0.13), residues: 3898 helix: 0.32 (0.12), residues: 1784 sheet: -1.78 (0.24), residues: 406 loop : -2.66 (0.14), residues: 1708 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 354 time to evaluate : 3.605 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 outliers start: 6 outliers final: 4 residues processed: 359 average time/residue: 0.4100 time to fit residues: 241.5888 Evaluate side-chains 265 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 261 time to evaluate : 3.605 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2970 time to fit residues: 6.9782 ------------------------------------------------------------------------------- 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: 0.8980 chunk 268 optimal weight: 0.9980 chunk 185 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 239 optimal weight: 10.0000 chunk 357 optimal weight: 0.9990 chunk 378 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 339 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS A 335 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1159 ASN ** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN D 355 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 31769 Z= 0.161 Angle : 0.583 8.306 42938 Z= 0.307 Chirality : 0.041 0.270 4766 Planarity : 0.004 0.061 5384 Dihedral : 5.916 88.476 4289 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.95 % Favored : 93.84 % Rotamer Outliers : 0.09 % 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: -1.11 (0.13), residues: 3898 helix: 0.95 (0.12), residues: 1780 sheet: -1.65 (0.24), residues: 412 loop : -2.42 (0.14), residues: 1706 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 377 time to evaluate : 3.816 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 outliers start: 3 outliers final: 2 residues processed: 380 average time/residue: 0.3680 time to fit residues: 235.7597 Evaluate side-chains 277 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 275 time to evaluate : 3.453 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3060 time to fit residues: 5.8151 ------------------------------------------------------------------------------- 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: 5.9990 chunk 215 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 282 optimal weight: 20.0000 chunk 156 optimal weight: 0.6980 chunk 323 optimal weight: 9.9990 chunk 261 optimal weight: 0.0010 chunk 0 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 chunk 340 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN B 355 ASN ** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS D 337 GLN D 355 ASN ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 31769 Z= 0.148 Angle : 0.557 8.382 42938 Z= 0.291 Chirality : 0.040 0.189 4766 Planarity : 0.004 0.065 5384 Dihedral : 5.555 84.982 4289 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.95 % Favored : 92.89 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.83 (0.14), residues: 3898 helix: 1.16 (0.12), residues: 1794 sheet: -1.51 (0.24), residues: 420 loop : -2.27 (0.15), residues: 1684 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 360 time to evaluate : 3.339 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 outliers start: 2 outliers final: 2 residues processed: 362 average time/residue: 0.3847 time to fit residues: 235.5115 Evaluate side-chains 275 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 273 time to evaluate : 3.718 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3188 time to fit residues: 6.1417 ------------------------------------------------------------------------------- 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: 5.9990 chunk 341 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 chunk 222 optimal weight: 0.1980 chunk 93 optimal weight: 1.9990 chunk 379 optimal weight: 1.9990 chunk 314 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 125 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS D 355 ASN ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 31769 Z= 0.140 Angle : 0.550 9.508 42938 Z= 0.285 Chirality : 0.040 0.175 4766 Planarity : 0.004 0.058 5384 Dihedral : 5.305 83.197 4289 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.93 % Favored : 93.92 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.65 (0.14), residues: 3898 helix: 1.28 (0.12), residues: 1800 sheet: -1.42 (0.24), residues: 420 loop : -2.16 (0.15), residues: 1678 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 354 time to evaluate : 3.563 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 outliers start: 2 outliers final: 2 residues processed: 356 average time/residue: 0.3779 time to fit residues: 228.7047 Evaluate side-chains 274 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 272 time to evaluate : 3.918 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3452 time to fit residues: 6.0520 ------------------------------------------------------------------------------- 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: 8.9990 chunk 42 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 276 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 319 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 377 optimal weight: 0.9990 chunk 236 optimal weight: 9.9990 chunk 230 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN B1159 ASN ** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN C 298 ASN D 355 ASN D1159 ASN ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 31769 Z= 0.247 Angle : 0.636 9.798 42938 Z= 0.334 Chirality : 0.041 0.162 4766 Planarity : 0.005 0.076 5384 Dihedral : 5.725 90.054 4289 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.29 % Favored : 91.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3898 helix: 1.14 (0.12), residues: 1796 sheet: -1.43 (0.25), residues: 380 loop : -2.13 (0.15), residues: 1722 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 3.655 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: 347 average time/residue: 0.3728 time to fit residues: 222.0191 Evaluate side-chains 267 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 3.528 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6880 ------------------------------------------------------------------------------- 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: 0.0470 chunk 150 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 240 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 186 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 296 optimal weight: 9.9990 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS A 642 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1159 ASN C 642 GLN D 355 ASN D1159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 31769 Z= 0.146 Angle : 0.571 8.966 42938 Z= 0.295 Chirality : 0.040 0.182 4766 Planarity : 0.004 0.066 5384 Dihedral : 5.380 83.985 4289 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.08 % Favored : 93.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3898 helix: 1.35 (0.13), residues: 1792 sheet: -1.53 (0.24), residues: 418 loop : -1.98 (0.15), residues: 1688 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 3.588 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: 369 average time/residue: 0.3896 time to fit residues: 244.7229 Evaluate side-chains 282 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 3.844 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0762 ------------------------------------------------------------------------------- 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: 7.9990 chunk 361 optimal weight: 4.9990 chunk 330 optimal weight: 7.9990 chunk 352 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 276 optimal weight: 5.9990 chunk 108 optimal weight: 0.0970 chunk 318 optimal weight: 7.9990 chunk 332 optimal weight: 9.9990 chunk 350 optimal weight: 0.9980 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1159 ASN ** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN D1159 ASN ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 31769 Z= 0.149 Angle : 0.574 10.478 42938 Z= 0.293 Chirality : 0.040 0.165 4766 Planarity : 0.004 0.074 5384 Dihedral : 5.282 83.786 4289 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.64 % 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 : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3898 helix: 1.38 (0.13), residues: 1790 sheet: -1.43 (0.24), residues: 432 loop : -1.99 (0.15), residues: 1676 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 4.045 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: 359 average time/residue: 0.3788 time to fit residues: 233.2149 Evaluate side-chains 285 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 3.319 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7665 ------------------------------------------------------------------------------- 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: 0.0770 chunk 372 optimal weight: 0.9990 chunk 227 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 258 optimal weight: 9.9990 chunk 390 optimal weight: 6.9990 chunk 359 optimal weight: 0.0270 chunk 310 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** A1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 GLN D 355 ASN ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 31769 Z= 0.189 Angle : 0.599 9.316 42938 Z= 0.308 Chirality : 0.041 0.271 4766 Planarity : 0.004 0.070 5384 Dihedral : 5.411 86.988 4289 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.16 % Favored : 92.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3898 helix: 1.34 (0.13), residues: 1788 sheet: -1.26 (0.25), residues: 386 loop : -2.03 (0.15), residues: 1724 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 3.322 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: 0 outliers final: 0 residues processed: 349 average time/residue: 0.3770 time to fit residues: 227.9442 Evaluate side-chains 275 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 3.565 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8813 ------------------------------------------------------------------------------- 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: 2.9990 chunk 331 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 311 optimal weight: 0.0000 chunk 130 optimal weight: 9.9990 chunk 319 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** A1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 GLN ** C1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.068066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.051823 restraints weight = 172360.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.053502 restraints weight = 101701.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.054685 restraints weight = 71407.394| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.6558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 31769 Z= 0.217 Angle : 0.621 11.485 42938 Z= 0.321 Chirality : 0.041 0.251 4766 Planarity : 0.004 0.069 5384 Dihedral : 5.623 91.546 4289 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.85 % Favored : 92.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3898 helix: 1.20 (0.12), residues: 1794 sheet: -1.37 (0.25), residues: 376 loop : -2.04 (0.15), residues: 1728 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5793.96 seconds wall clock time: 107 minutes 13.81 seconds (6433.81 seconds total)