Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 06:52:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wek_8819/04_2023/5wek_8819_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wek_8819/04_2023/5wek_8819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wek_8819/04_2023/5wek_8819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wek_8819/04_2023/5wek_8819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wek_8819/04_2023/5wek_8819_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wek_8819/04_2023/5wek_8819_updated.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 144 5.16 5 C 17648 2.51 5 N 4530 2.21 5 O 5130 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 660": "NH1" <-> "NH2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A ARG 1005": "NH1" <-> "NH2" Residue "A ARG 1006": "NH1" <-> "NH2" Residue "A ARG 1090": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 309": "NH1" <-> "NH2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ARG 661": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 692": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 309": "NH1" <-> "NH2" Residue "C TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 660": "NH1" <-> "NH2" Residue "C ARG 661": "NH1" <-> "NH2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 692": "NH1" <-> "NH2" Residue "C ARG 1005": "NH1" <-> "NH2" Residue "C ARG 1006": "NH1" <-> "NH2" Residue "C ARG 1090": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 309": "NH1" <-> "NH2" Residue "D TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "D ARG 661": "NH1" <-> "NH2" Residue "D ARG 675": "NH1" <-> "NH2" Residue "D ARG 692": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 27468 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7555 Classifications: {'peptide': 962} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 5, 'PTRANS': 21, 'TRANS': 935} Chain breaks: 5 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 6125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6125 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 757} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 7555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7555 Classifications: {'peptide': 962} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 5, 'PTRANS': 21, 'TRANS': 935} Chain breaks: 5 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 6125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6125 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 757} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.68, per 1000 atoms: 0.50 Number of scatterers: 27468 At special positions: 0 Unit cell: (118.58, 161.7, 194.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 4 15.00 F 12 9.00 O 5130 8.00 N 4530 7.00 C 17648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A1099 " - pdb=" SG CYS A1110 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C1099 " - pdb=" SG CYS C1110 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.50 Conformation dependent library (CDL) restraints added in 4.4 seconds 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 38 sheets defined 42.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 Processing helix chain 'A' and resid 55 through 68 removed outlier: 3.584A pdb=" N GLN A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.726A pdb=" N THR A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.535A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.541A pdb=" N SER A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 211 Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.778A pdb=" N PHE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 302 removed outlier: 3.631A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.533A pdb=" N GLU A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 removed outlier: 3.817A 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 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 514 through 517 No H-bonds generated for 'chain 'A' and resid 514 through 517' Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.796A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 541 removed outlier: 4.592A pdb=" N VAL A 538 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 597 through 629 removed outlier: 3.604A pdb=" N LEU A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 612 " --> pdb=" O PHE A 608 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 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 695 removed outlier: 3.568A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 742 through 753 removed outlier: 3.571A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 778 through 780 No H-bonds generated for 'chain 'A' and resid 778 through 780' Processing helix chain 'A' and resid 789 through 819 removed outlier: 3.746A pdb=" N ALA A 793 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY A 794 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 798 " --> pdb=" O VAL A 795 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 800 " --> pdb=" O TYR A 797 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY A 801 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 804 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET A 807 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 808 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL A 809 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 811 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 812 " --> pdb=" O VAL A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1027 Processing helix chain 'A' and resid 1121 through 1153 removed outlier: 3.569A pdb=" N LEU A1127 " --> pdb=" O GLY A1123 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A1130 " --> pdb=" O TRP A1126 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A1138 " --> pdb=" O LEU A1134 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A1139 " --> pdb=" O TYR A1135 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1140 " --> pdb=" O ILE A1136 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A1141 " --> pdb=" O LEU A1137 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A1142 " --> pdb=" O LEU A1138 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A1145 " --> pdb=" O VAL A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1194 removed outlier: 3.565A pdb=" N PHE A1169 " --> pdb=" O PHE A1165 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A1170 " --> pdb=" O ALA A1166 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A1174 " --> pdb=" O THR A1170 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A1176 " --> pdb=" O LEU A1172 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A1179 " --> pdb=" O LEU A1175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A1185 " --> pdb=" O HIS A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1227 removed outlier: 3.554A pdb=" N GLY A1215 " --> pdb=" O CYS A1211 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A1216 " --> pdb=" O LEU A1212 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A1217 " --> pdb=" O ALA A1213 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A1218 " --> pdb=" O TRP A1214 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A1223 " --> pdb=" O CYS A1219 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR A1226 " --> pdb=" O ALA A1222 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A1227 " --> pdb=" O ALA A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1232 No H-bonds generated for 'chain 'A' and resid 1229 through 1232' Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.584A pdb=" N GLN B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.726A pdb=" N THR B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 removed outlier: 3.534A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.541A pdb=" N SER B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 211 Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.780A pdb=" N PHE B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 302 removed outlier: 3.632A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 334 removed outlier: 3.532A pdb=" N GLU B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 420 removed outlier: 3.817A pdb=" N ARG B 420 " --> pdb=" O GLY B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 417 through 420' Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.773A pdb=" N PHE B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 517' Processing helix chain 'B' and resid 523 through 531 removed outlier: 3.795A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 541 removed outlier: 4.592A pdb=" N VAL B 538 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'B' and resid 597 through 626 removed outlier: 3.605A pdb=" N LEU B 610 " --> pdb=" O TRP B 606 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE B 612 " --> pdb=" O PHE B 608 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 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 695 removed outlier: 3.569A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 712 Processing helix chain 'B' and resid 742 through 753 removed outlier: 3.572A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 794 through 816 removed outlier: 3.569A pdb=" N ILE B 798 " --> pdb=" O VAL B 795 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 800 " --> pdb=" O TYR B 797 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY B 801 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 804 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET B 807 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 808 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL B 809 " --> pdb=" O ALA B 806 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 811 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 812 " --> pdb=" O VAL B 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 35 Processing helix chain 'C' and resid 55 through 68 removed outlier: 3.584A pdb=" N GLN C 65 " --> pdb=" O ALA C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.726A pdb=" N THR C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER C 87 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 128 removed outlier: 3.535A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 155 Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.541A pdb=" N SER C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 211 Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.780A pdb=" N PHE C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 302 removed outlier: 3.631A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 334 removed outlier: 3.534A pdb=" N GLU C 330 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 removed outlier: 3.819A 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 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 514 through 517 No H-bonds generated for 'chain 'C' and resid 514 through 517' Processing helix chain 'C' and resid 523 through 531 removed outlier: 3.794A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 541 removed outlier: 4.592A pdb=" N VAL C 538 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 581 Processing helix chain 'C' and resid 597 through 629 removed outlier: 3.604A pdb=" N LEU C 610 " --> pdb=" O TRP C 606 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 612 " --> pdb=" O PHE C 608 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 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 695 removed outlier: 3.569A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 712 Processing helix chain 'C' and resid 742 through 753 removed outlier: 3.570A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 767 Processing helix chain 'C' and resid 778 through 780 No H-bonds generated for 'chain 'C' and resid 778 through 780' Processing helix chain 'C' and resid 789 through 818 removed outlier: 4.483A pdb=" N VAL C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR C 797 " --> pdb=" O ALA C 793 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE C 798 " --> pdb=" O GLY C 794 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 799 " --> pdb=" O VAL C 795 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 810 " --> pdb=" O ALA C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1027 Processing helix chain 'C' and resid 1121 through 1153 removed outlier: 3.569A pdb=" N LEU C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C1130 " --> pdb=" O TRP C1126 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C1138 " --> pdb=" O LEU C1134 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C1139 " --> pdb=" O TYR C1135 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C1140 " --> pdb=" O ILE C1136 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C1141 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY C1142 " --> pdb=" O LEU C1138 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE C1143 " --> pdb=" O LEU C1139 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C1145 " --> pdb=" O VAL C1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1194 removed outlier: 3.565A pdb=" N PHE C1169 " --> pdb=" O PHE C1165 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR C1170 " --> pdb=" O ALA C1166 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C1174 " --> pdb=" O THR C1170 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C1176 " --> pdb=" O LEU C1172 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL C1179 " --> pdb=" O LEU C1175 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C1185 " --> pdb=" O HIS C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1209 through 1227 removed outlier: 3.554A pdb=" N GLY C1215 " --> pdb=" O CYS C1211 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C1216 " --> pdb=" O LEU C1212 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE C1217 " --> pdb=" O ALA C1213 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR C1218 " --> pdb=" O TRP C1214 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C1223 " --> pdb=" O CYS C1219 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR C1226 " --> pdb=" O ALA C1222 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C1227 " --> pdb=" O ALA C1223 " (cutoff:3.500A) Processing helix chain 'C' and resid 1229 through 1232 No H-bonds generated for 'chain 'C' and resid 1229 through 1232' Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 55 through 68 removed outlier: 3.584A pdb=" N GLN D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.726A pdb=" N THR D 86 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 removed outlier: 3.536A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 Processing helix chain 'D' and resid 175 through 186 removed outlier: 3.541A pdb=" N SER D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 211 Processing helix chain 'D' and resid 253 through 262 removed outlier: 3.780A pdb=" N PHE D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 302 removed outlier: 3.632A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 334 removed outlier: 3.533A pdb=" N GLU D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 420 removed outlier: 3.818A pdb=" N ARG D 420 " --> pdb=" O GLY D 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 417 through 420' Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 514 through 517 No H-bonds generated for 'chain 'D' and resid 514 through 517' Processing helix chain 'D' and resid 523 through 531 removed outlier: 3.795A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 541 removed outlier: 4.591A pdb=" N VAL D 538 " --> pdb=" O GLY D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 581 Processing helix chain 'D' and resid 597 through 626 removed outlier: 3.605A pdb=" N LEU D 610 " --> pdb=" O TRP D 606 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 612 " --> pdb=" O PHE D 608 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 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 695 removed outlier: 3.569A pdb=" N VAL D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 712 Processing helix chain 'D' and resid 742 through 753 removed outlier: 3.572A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 790 through 816 removed outlier: 4.289A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 799 " --> pdb=" O VAL D 795 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET D 807 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 11 through 16 removed outlier: 6.302A pdb=" N ARG A 42 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE A 14 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR A 44 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY A 16 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N HIS A 46 " --> pdb=" O GLY A 16 " (cutoff:3.500A) No H-bonds generated for sheet with id= A 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 132 through 137 removed outlier: 5.935A pdb=" N GLN A 159 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR A 135 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR A 161 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR A 137 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 163 " --> pdb=" O TYR A 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 191 through 194 removed outlier: 6.428A pdb=" N HIS A 219 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU A 194 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLU A 241 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE A 222 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER A 243 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 359 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 338 through 340 Processing sheet with id= F, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= G, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= H, first strand: chain 'A' and resid 720 through 723 removed outlier: 4.068A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1033 through 1036 removed outlier: 3.552A pdb=" N THR A1093 " --> pdb=" O CYS A1033 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG A1090 " --> pdb=" O GLU A1101 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 494 through 498 removed outlier: 6.843A pdb=" N TYR A 732 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER A 497 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS A 730 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 11 through 16 removed outlier: 6.302A pdb=" N ARG B 42 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE B 14 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR B 44 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY B 16 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N HIS B 46 " --> pdb=" O GLY B 16 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= M, first strand: chain 'B' and resid 132 through 137 removed outlier: 5.936A pdb=" N GLN B 159 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR B 135 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR B 161 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR B 137 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE B 163 " --> pdb=" O TYR B 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 191 through 194 removed outlier: 6.427A pdb=" N HIS B 219 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU B 194 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU B 241 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE B 222 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER B 243 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN B 359 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 338 through 340 Processing sheet with id= P, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= Q, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= R, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.069A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 494 through 498 removed outlier: 6.843A pdb=" N TYR B 732 " --> pdb=" O PHE B 495 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER B 497 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS B 730 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 11 through 16 removed outlier: 6.302A pdb=" N ARG C 42 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE C 14 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N THR C 44 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY C 16 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N HIS C 46 " --> pdb=" O GLY C 16 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= V, first strand: chain 'C' and resid 132 through 137 removed outlier: 5.935A pdb=" N GLN C 159 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR C 135 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR C 161 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR C 137 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE C 163 " --> pdb=" O TYR C 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'C' and resid 191 through 194 removed outlier: 6.427A pdb=" N HIS C 219 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU C 194 " --> pdb=" O HIS C 219 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU C 241 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE C 222 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER C 243 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN C 359 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 338 through 340 Processing sheet with id= Y, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= Z, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= AA, first strand: chain 'C' and resid 720 through 723 removed outlier: 4.069A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 1033 through 1036 removed outlier: 3.551A pdb=" N THR C1093 " --> pdb=" O CYS C1033 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG C1090 " --> pdb=" O GLU C1101 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.843A pdb=" N TYR C 732 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER C 497 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS C 730 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 11 through 16 removed outlier: 6.303A pdb=" N ARG D 42 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE D 14 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR D 44 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY D 16 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N HIS D 46 " --> pdb=" O GLY D 16 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'D' and resid 96 through 98 Processing sheet with id= AF, first strand: chain 'D' and resid 132 through 137 removed outlier: 5.934A pdb=" N GLN D 159 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR D 135 " --> pdb=" O GLN D 159 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR D 161 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR D 137 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE D 163 " --> pdb=" O TYR D 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'D' and resid 191 through 194 removed outlier: 6.427A pdb=" N HIS D 219 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU D 194 " --> pdb=" O HIS D 219 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE D 221 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU D 241 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE D 222 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER D 243 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN D 359 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 338 through 340 Processing sheet with id= AI, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= AJ, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= AK, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.069A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'D' and resid 494 through 498 removed outlier: 6.843A pdb=" N TYR D 732 " --> pdb=" O PHE D 495 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER D 497 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS D 730 " --> pdb=" O SER D 497 " (cutoff:3.500A) 976 hydrogen bonds defined for protein. 2766 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: 9.83 Time building geometry restraints manager: 12.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4487 1.30 - 1.44: 7653 1.44 - 1.58: 15676 1.58 - 1.72: 8 1.72 - 1.86: 234 Bond restraints: 28058 Sorted by residual: bond pdb=" C VAL A 792 " pdb=" N ALA A 793 " ideal model delta sigma weight residual 1.335 1.539 -0.204 1.38e-02 5.25e+03 2.19e+02 bond pdb=" C PRO D 512 " pdb=" N GLY D 513 " ideal model delta sigma weight residual 1.331 1.523 -0.192 1.46e-02 4.69e+03 1.73e+02 bond pdb=" C VAL C 792 " pdb=" N ALA C 793 " ideal model delta sigma weight residual 1.335 1.165 0.170 1.38e-02 5.25e+03 1.51e+02 bond pdb=" C ILE A 612 " pdb=" N ILE A 613 " ideal model delta sigma weight residual 1.333 1.464 -0.131 1.24e-02 6.50e+03 1.11e+02 bond pdb=" C ILE D 612 " pdb=" N ILE D 613 " ideal model delta sigma weight residual 1.335 1.454 -0.120 1.15e-02 7.56e+03 1.09e+02 ... (remaining 28053 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.48: 421 105.48 - 113.02: 15151 113.02 - 120.56: 11927 120.56 - 128.10: 10244 128.10 - 135.64: 213 Bond angle restraints: 37956 Sorted by residual: angle pdb=" CA VAL D 792 " pdb=" C VAL D 792 " pdb=" N ALA D 793 " ideal model delta sigma weight residual 118.55 106.39 12.16 8.60e-01 1.35e+00 2.00e+02 angle pdb=" O VAL B 792 " pdb=" C VAL B 792 " pdb=" N ALA B 793 " ideal model delta sigma weight residual 122.20 108.80 13.40 1.00e+00 1.00e+00 1.79e+02 angle pdb=" CA VAL B 792 " pdb=" C VAL B 792 " pdb=" N ALA B 793 " ideal model delta sigma weight residual 118.56 129.17 -10.61 9.90e-01 1.02e+00 1.15e+02 angle pdb=" O VAL D 792 " pdb=" C VAL D 792 " pdb=" N ALA D 793 " ideal model delta sigma weight residual 122.23 131.70 -9.47 9.80e-01 1.04e+00 9.34e+01 angle pdb=" C VAL D 792 " pdb=" N ALA D 793 " pdb=" CA ALA D 793 " ideal model delta sigma weight residual 121.14 108.91 12.23 1.75e+00 3.27e-01 4.89e+01 ... (remaining 37951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.33: 16264 21.33 - 42.66: 274 42.66 - 64.00: 37 64.00 - 85.33: 7 85.33 - 106.66: 2 Dihedral angle restraints: 16584 sinusoidal: 6560 harmonic: 10024 Sorted by residual: dihedral pdb=" CA GLY A1207 " pdb=" C GLY A1207 " pdb=" N TRP A1208 " pdb=" CA TRP A1208 " ideal model delta harmonic sigma weight residual 180.00 73.34 106.66 0 5.00e+00 4.00e-02 4.55e+02 dihedral pdb=" CA GLY C1207 " pdb=" C GLY C1207 " pdb=" N TRP C1208 " pdb=" CA TRP C1208 " ideal model delta harmonic sigma weight residual 180.00 73.38 106.62 0 5.00e+00 4.00e-02 4.55e+02 dihedral pdb=" CA PRO D 512 " pdb=" C PRO D 512 " pdb=" N GLY D 513 " pdb=" CA GLY D 513 " ideal model delta harmonic sigma weight residual -180.00 -100.92 -79.08 0 5.00e+00 4.00e-02 2.50e+02 ... (remaining 16581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3408 0.059 - 0.118: 734 0.118 - 0.177: 61 0.177 - 0.236: 11 0.236 - 0.295: 6 Chirality restraints: 4220 Sorted by residual: chirality pdb=" CG LEU A 596 " pdb=" CB LEU A 596 " pdb=" CD1 LEU A 596 " pdb=" CD2 LEU A 596 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CG LEU B 596 " pdb=" CB LEU B 596 " pdb=" CD1 LEU B 596 " pdb=" CD2 LEU B 596 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CG LEU D 596 " pdb=" CB LEU D 596 " pdb=" CD1 LEU D 596 " pdb=" CD2 LEU D 596 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 4217 not shown) Planarity restraints: 4756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 612 " 0.042 2.00e-02 2.50e+03 8.35e-02 6.97e+01 pdb=" C ILE C 612 " -0.144 2.00e-02 2.50e+03 pdb=" O ILE C 612 " 0.052 2.00e-02 2.50e+03 pdb=" N ILE C 613 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 612 " 0.039 2.00e-02 2.50e+03 7.68e-02 5.90e+01 pdb=" C ILE B 612 " -0.133 2.00e-02 2.50e+03 pdb=" O ILE B 612 " 0.047 2.00e-02 2.50e+03 pdb=" N ILE B 613 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 817 " 0.030 2.00e-02 2.50e+03 6.06e-02 3.68e+01 pdb=" C LYS A 817 " -0.105 2.00e-02 2.50e+03 pdb=" O LYS A 817 " 0.040 2.00e-02 2.50e+03 pdb=" N SER A 818 " 0.035 2.00e-02 2.50e+03 ... (remaining 4753 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6717 2.78 - 3.31: 25359 3.31 - 3.84: 46369 3.84 - 4.37: 56133 4.37 - 4.90: 89887 Nonbonded interactions: 224465 Sorted by model distance: nonbonded pdb=" OH TYR C 77 " pdb=" O PHE C 101 " model vdw 2.248 2.440 nonbonded pdb=" OH TYR D 77 " pdb=" O PHE D 101 " model vdw 2.248 2.440 nonbonded pdb=" OH TYR A 77 " pdb=" O PHE A 101 " model vdw 2.248 2.440 nonbonded pdb=" OH TYR B 77 " pdb=" O PHE B 101 " model vdw 2.249 2.440 nonbonded pdb=" NH1 ARG A 485 " pdb=" OAA ZK1 A1301 " model vdw 2.289 2.520 ... (remaining 224460 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.220 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 68.980 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.130 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 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 : 0.006 0.204 28058 Z= 0.412 Angle : 0.930 17.830 37956 Z= 0.542 Chirality : 0.047 0.295 4220 Planarity : 0.007 0.094 4756 Dihedral : 9.247 106.660 10146 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.84 % Favored : 94.93 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -4.07 (0.11), residues: 3452 helix: -3.23 (0.08), residues: 1522 sheet: -2.76 (0.23), residues: 420 loop : -1.85 (0.14), residues: 1510 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 224 average time/residue: 0.2206 time to fit residues: 64.0966 Evaluate side-chains 113 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2058 Evaluate side-chains 178 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 176 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 178 average time/residue: 0.2258 time to fit residues: 49.9396 Evaluate side-chains 74 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.737 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 0.0170 chunk 263 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 140 optimal weight: 0.3980 chunk 272 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 chunk 316 optimal weight: 9.9990 overall best weight: 2.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN A 298 ASN A 412 HIS A1016 ASN A1092 HIS A1229 ASN Total number of N/Q/H flips: 6 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 392 GLN D 412 HIS ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 28058 Z= 0.215 Angle : 0.644 14.912 37956 Z= 0.344 Chirality : 0.044 0.237 4220 Planarity : 0.006 0.101 4756 Dihedral : 6.829 85.091 3786 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.92 % Favored : 94.90 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.13), residues: 3452 helix: -1.30 (0.11), residues: 1580 sheet: -2.37 (0.21), residues: 450 loop : -1.48 (0.16), residues: 1422 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 0.934 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: 2 outliers final: 0 residues processed: 143 average time/residue: 0.2116 time to fit residues: 40.5907 Evaluate side-chains 89 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2705 Evaluate side-chains 93 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 92 average time/residue: 0.1522 time to fit residues: 19.7478 Evaluate side-chains 56 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.753 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 263 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 316 optimal weight: 2.9990 chunk 342 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 chunk 313 optimal weight: 0.1980 chunk 107 optimal weight: 0.0170 chunk 253 optimal weight: 5.9990 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN A1092 HIS A1181 HIS A1229 ASN Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 147 GLN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 28058 Z= 0.182 Angle : 0.594 14.937 37956 Z= 0.312 Chirality : 0.043 0.383 4220 Planarity : 0.005 0.070 4756 Dihedral : 6.327 78.893 3786 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.68 % Favored : 94.15 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % 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: -1.89 (0.13), residues: 3452 helix: -0.70 (0.12), residues: 1584 sheet: -2.16 (0.22), residues: 444 loop : -1.43 (0.16), residues: 1424 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.1884 time to fit residues: 32.6493 Evaluate side-chains 89 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2010 Evaluate side-chains 84 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1608 time to fit residues: 18.9630 Evaluate side-chains 55 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.738 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 2.9990 chunk 238 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 151 optimal weight: 0.0040 chunk 212 optimal weight: 6.9990 chunk 317 optimal weight: 10.0000 chunk 336 optimal weight: 0.0270 chunk 165 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 overall best weight: 3.2056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN A1092 HIS A1181 HIS A1229 ASN Total number of N/Q/H flips: 5 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 28058 Z= 0.220 Angle : 0.610 12.361 37956 Z= 0.323 Chirality : 0.042 0.260 4220 Planarity : 0.004 0.061 4756 Dihedral : 6.127 76.550 3786 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.97 % Favored : 93.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3452 helix: -0.26 (0.12), residues: 1578 sheet: -2.09 (0.22), residues: 438 loop : -1.31 (0.16), residues: 1436 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1793 time to fit residues: 29.5040 Evaluate side-chains 90 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.798 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2756 Evaluate side-chains 76 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.772 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1579 time to fit residues: 17.3514 Evaluate side-chains 51 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 250 optimal weight: 8.9990 chunk 138 optimal weight: 0.0970 chunk 287 optimal weight: 10.0000 chunk 232 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 301 optimal weight: 6.9990 chunk 84 optimal weight: 0.2980 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN A1092 HIS A1181 HIS A1229 ASN Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 28058 Z= 0.212 Angle : 0.594 12.986 37956 Z= 0.313 Chirality : 0.042 0.306 4220 Planarity : 0.005 0.090 4756 Dihedral : 6.139 80.817 3786 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.32 % Favored : 93.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % 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: -1.28 (0.14), residues: 3452 helix: 0.04 (0.13), residues: 1580 sheet: -1.85 (0.23), residues: 444 loop : -1.41 (0.16), residues: 1428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1805 time to fit residues: 29.7947 Evaluate side-chains 85 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2411 Evaluate side-chains 68 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1542 time to fit residues: 15.0740 Evaluate side-chains 51 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 6.9990 chunk 302 optimal weight: 0.0050 chunk 66 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 336 optimal weight: 10.0000 chunk 279 optimal weight: 0.0770 chunk 155 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 overall best weight: 2.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1092 HIS A1181 HIS A1229 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.6164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 28058 Z= 0.189 Angle : 0.577 12.053 37956 Z= 0.305 Chirality : 0.042 0.336 4220 Planarity : 0.004 0.058 4756 Dihedral : 5.943 78.713 3786 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.20 % Favored : 93.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3452 helix: 0.24 (0.13), residues: 1584 sheet: -1.81 (0.23), residues: 446 loop : -1.43 (0.16), residues: 1422 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.957 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: 112 average time/residue: 0.1797 time to fit residues: 28.4921 Evaluate side-chains 77 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2676 Evaluate side-chains 66 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1871 time to fit residues: 16.8736 Evaluate side-chains 47 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.758 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 245 optimal weight: 0.0040 chunk 190 optimal weight: 9.9990 chunk 283 optimal weight: 4.9990 chunk 188 optimal weight: 0.0270 chunk 335 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 204 optimal weight: 20.0000 chunk 154 optimal weight: 0.0060 overall best weight: 1.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 HIS A1181 HIS A1229 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 28058 Z= 0.157 Angle : 0.567 13.394 37956 Z= 0.295 Chirality : 0.042 0.344 4220 Planarity : 0.004 0.089 4756 Dihedral : 5.724 72.407 3786 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.62 % Favored : 94.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3452 helix: 0.41 (0.13), residues: 1580 sheet: -1.71 (0.24), residues: 446 loop : -1.33 (0.16), residues: 1426 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1748 time to fit residues: 27.2371 Evaluate side-chains 78 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2198 Evaluate side-chains 76 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1559 time to fit residues: 16.5435 Evaluate side-chains 45 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.701 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 10.0000 chunk 133 optimal weight: 0.0370 chunk 200 optimal weight: 0.0980 chunk 101 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 213 optimal weight: 0.3980 chunk 228 optimal weight: 10.0000 chunk 165 optimal weight: 0.0170 chunk 31 optimal weight: 10.0000 chunk 263 optimal weight: 6.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1189 GLN A1229 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.6565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 28058 Z= 0.146 Angle : 0.586 13.600 37956 Z= 0.297 Chirality : 0.042 0.354 4220 Planarity : 0.004 0.078 4756 Dihedral : 5.518 68.151 3786 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.27 % Favored : 94.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3452 helix: 0.40 (0.13), residues: 1576 sheet: -1.65 (0.24), residues: 436 loop : -1.24 (0.17), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1958 time to fit residues: 30.5285 Evaluate side-chains 75 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2328 Evaluate side-chains 73 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1806 time to fit residues: 18.0373 Evaluate side-chains 50 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.747 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 5.9990 chunk 321 optimal weight: 0.0870 chunk 293 optimal weight: 0.0870 chunk 312 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 245 optimal weight: 0.8980 chunk 95 optimal weight: 30.0000 chunk 282 optimal weight: 3.9990 chunk 295 optimal weight: 7.9990 chunk 311 optimal weight: 9.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1229 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 28058 Z= 0.153 Angle : 0.594 13.034 37956 Z= 0.305 Chirality : 0.043 0.349 4220 Planarity : 0.004 0.072 4756 Dihedral : 5.454 66.050 3786 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3452 helix: 0.49 (0.13), residues: 1580 sheet: -1.55 (0.24), residues: 432 loop : -1.25 (0.16), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1788 time to fit residues: 27.0460 Evaluate side-chains 76 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2602 Evaluate side-chains 68 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.887 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1493 time to fit residues: 14.6686 Evaluate side-chains 44 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 0.6980 chunk 330 optimal weight: 8.9990 chunk 201 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 229 optimal weight: 0.3980 chunk 346 optimal weight: 9.9990 chunk 319 optimal weight: 0.3980 chunk 276 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 213 optimal weight: 0.0770 chunk 169 optimal weight: 0.0770 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS A1229 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.6927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 28058 Z= 0.153 Angle : 0.601 13.100 37956 Z= 0.304 Chirality : 0.043 0.341 4220 Planarity : 0.004 0.079 4756 Dihedral : 5.378 61.779 3786 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.39 % Favored : 94.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3452 helix: 0.49 (0.13), residues: 1568 sheet: -1.56 (0.24), residues: 434 loop : -1.28 (0.16), residues: 1450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1801 time to fit residues: 27.2511 Evaluate side-chains 83 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.964 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3019 Evaluate side-chains 66 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.802 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1775 time to fit residues: 16.4015 Evaluate side-chains 48 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.733 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 0.6980 chunk 294 optimal weight: 0.0770 chunk 84 optimal weight: 8.9990 chunk 254 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 283 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 50 optimal weight: 0.0010 overall best weight: 1.7548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1229 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.072021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.057263 restraints weight = 47034.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.058732 restraints weight = 28447.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.059747 restraints weight = 20080.094| |-----------------------------------------------------------------------------| r_work (final): 0.3269 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.064344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.050885 restraints weight = 42086.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.052075 restraints weight = 28481.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.052842 restraints weight = 21362.661| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.7105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 28058 Z= 0.171 Angle : 0.601 12.339 37956 Z= 0.308 Chirality : 0.042 0.318 4220 Planarity : 0.004 0.078 4756 Dihedral : 5.237 59.069 3786 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.68 % Favored : 94.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3452 helix: 0.49 (0.13), residues: 1582 sheet: -1.51 (0.25), residues: 436 loop : -1.30 (0.16), residues: 1434 =============================================================================== Job complete usr+sys time: 3396.12 seconds wall clock time: 65 minutes 14.20 seconds (3914.20 seconds total)