Starting phenix.real_space_refine on Mon Sep 14 03:09:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5wek_8819/09_2026/5wek_8819.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wek_8819/09_2026/5wek_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/5wek_8819/09_2026/5wek_8819.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5wek_8819/09_2026/5wek_8819.cif" model { file = "/net/cci-nas-00/data/ceres_data/5wek_8819/09_2026/5wek_8819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wek_8819/09_2026/5wek_8819.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5wek_8819/09_2026/5wek_8819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wek_8819/09_2026/5wek_8819.map" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 5.95, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 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: 2.31 Conformation dependent library (CDL) restraints added in 1.2 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... Secondary structure from input PDB file: 130 helices and 38 sheets defined 48.9% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 54 through 69 removed outlier: 3.584A pdb=" N GLN A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 93 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 117 through 129 removed outlier: 3.535A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.541A pdb=" N SER A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.778A pdb=" N PHE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 303 removed outlier: 3.631A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.640A pdb=" N VAL A 327 " --> pdb=" O TRP A 323 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.693A pdb=" N LEU A 390 " --> pdb=" O THR A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.774A pdb=" N PHE A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 518' Processing helix chain 'A' and resid 522 through 532 removed outlier: 3.796A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 536 through 542 Processing helix chain 'A' and resid 576 through 582 Processing helix chain 'A' and resid 596 through 630 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 635 through 642 removed outlier: 3.523A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 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 713 Processing helix chain 'A' and resid 742 through 754 removed outlier: 3.571A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 777 through 781 removed outlier: 3.884A pdb=" N LYS A 781 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 795 through 820 removed outlier: 3.551A pdb=" N LEU A 799 " --> pdb=" O VAL A 795 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1028 Processing helix chain 'A' and resid 1120 through 1154 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 1159 through 1195 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 1208 through 1228 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 1228 through 1233 removed outlier: 4.317A pdb=" N LYS A1233 " --> pdb=" O ASN A1229 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 54 through 69 removed outlier: 3.584A pdb=" N GLN B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 93 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 117 through 129 removed outlier: 3.534A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.541A pdb=" N SER B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.780A pdb=" N PHE B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 303 removed outlier: 3.632A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 335 removed outlier: 3.641A pdb=" N VAL B 327 " --> pdb=" O TRP B 323 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 512 through 518 removed outlier: 3.773A pdb=" N PHE B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 532 removed outlier: 3.795A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 576 through 582 Processing helix chain 'B' and resid 596 through 627 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) removed outlier: 4.218A pdb=" N GLU B 627 " --> pdb=" O PHE B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.523A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 696 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 713 Processing helix chain 'B' and resid 742 through 754 removed outlier: 3.572A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 789 through 794 removed outlier: 3.907A pdb=" N ALA B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 789 through 794' Processing helix chain 'B' and resid 795 through 817 removed outlier: 3.551A pdb=" N LEU B 799 " --> pdb=" O VAL B 795 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 54 through 69 removed outlier: 3.584A pdb=" N GLN C 65 " --> pdb=" O ALA C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 93 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 117 through 129 removed outlier: 3.535A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 156 Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.541A pdb=" N SER C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.780A pdb=" N PHE C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 303 removed outlier: 3.631A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 335 removed outlier: 3.640A pdb=" N VAL C 327 " --> pdb=" O TRP C 323 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C 330 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN C 335 " --> pdb=" O ARG C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.693A pdb=" N LEU C 390 " --> pdb=" O THR C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.774A pdb=" N PHE C 517 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 518 " --> pdb=" O VAL C 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 513 through 518' Processing helix chain 'C' and resid 522 through 532 removed outlier: 3.794A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 535 No H-bonds generated for 'chain 'C' and resid 533 through 535' Processing helix chain 'C' and resid 536 through 542 Processing helix chain 'C' and resid 576 through 582 Processing helix chain 'C' and resid 596 through 630 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 635 through 642 removed outlier: 3.523A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 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 713 Processing helix chain 'C' and resid 742 through 754 removed outlier: 3.570A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 777 through 781 removed outlier: 3.884A pdb=" N LYS C 781 " --> pdb=" O SER C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 795 through 819 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 1028 Processing helix chain 'C' and resid 1120 through 1154 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 1159 through 1195 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 1208 through 1228 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 1228 through 1233 removed outlier: 4.317A pdb=" N LYS C1233 " --> pdb=" O ASN C1229 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 54 through 69 removed outlier: 3.584A pdb=" N GLN D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 93 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 117 through 129 removed outlier: 3.536A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 156 Processing helix chain 'D' and resid 174 through 185 removed outlier: 3.541A pdb=" N SER D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.780A pdb=" N PHE D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 303 removed outlier: 3.632A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 335 removed outlier: 3.641A pdb=" N VAL D 327 " --> pdb=" O TRP D 323 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN D 335 " --> pdb=" O ARG D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.773A pdb=" N PHE D 517 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 518' Processing helix chain 'D' and resid 522 through 532 removed outlier: 3.795A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 576 through 582 Processing helix chain 'D' and resid 596 through 627 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) removed outlier: 4.216A pdb=" N GLU D 627 " --> pdb=" O PHE D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.523A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 696 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 713 Processing helix chain 'D' and resid 742 through 754 removed outlier: 3.572A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 789 through 794 removed outlier: 4.289A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 817 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=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.240A pdb=" N ILE A 12 " --> pdb=" O THR A 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 74 removed outlier: 6.418A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 137 Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 194 removed outlier: 6.453A pdb=" N TYR A 220 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N PHE A 245 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE A 222 " --> pdb=" O PHE A 245 " (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=AA5, first strand: chain 'A' and resid 338 through 340 removed outlier: 3.522A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 440 through 444 Processing sheet with id=AA7, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'A' and resid 489 through 498 removed outlier: 6.746A pdb=" N SER A 492 " --> pdb=" O THR A 736 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N THR A 736 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE A 734 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 646 through 648 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) removed outlier: 8.952A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AB1, 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=AB2, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.240A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 73 through 74 removed outlier: 6.419A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 132 through 137 Processing sheet with id=AB5, first strand: chain 'B' and resid 191 through 194 removed outlier: 6.452A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N PHE B 245 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ILE B 222 " --> pdb=" O PHE B 245 " (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=AB6, first strand: chain 'B' and resid 338 through 340 removed outlier: 3.520A pdb=" N LYS B 346 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 440 through 444 Processing sheet with id=AB8, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'B' and resid 489 through 498 removed outlier: 6.747A pdb=" N SER B 492 " --> pdb=" O THR B 736 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N THR B 736 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE B 734 " --> pdb=" O PRO B 494 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 646 through 648 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) removed outlier: 8.951A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.240A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 73 through 74 removed outlier: 6.419A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 132 through 137 Processing sheet with id=AC5, first strand: chain 'C' and resid 191 through 194 removed outlier: 6.453A pdb=" N TYR C 220 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N PHE C 245 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE C 222 " --> pdb=" O PHE C 245 " (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=AC6, first strand: chain 'C' and resid 338 through 340 removed outlier: 3.521A pdb=" N LYS C 346 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 440 through 444 Processing sheet with id=AC8, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AC9, first strand: chain 'C' and resid 489 through 498 removed outlier: 6.747A pdb=" N SER C 492 " --> pdb=" O THR C 736 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N THR C 736 " --> pdb=" O SER C 492 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE C 734 " --> pdb=" O PRO C 494 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 646 through 648 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) removed outlier: 8.952A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AD2, 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=AD3, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.240A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 73 through 74 removed outlier: 6.419A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 132 through 137 Processing sheet with id=AD6, first strand: chain 'D' and resid 191 through 194 removed outlier: 6.452A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N PHE D 245 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE D 222 " --> pdb=" O PHE D 245 " (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=AD7, first strand: chain 'D' and resid 338 through 340 removed outlier: 3.520A pdb=" N LYS D 346 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 440 through 444 Processing sheet with id=AD9, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AE1, first strand: chain 'D' and resid 489 through 498 removed outlier: 6.747A pdb=" N SER D 492 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N THR D 736 " --> pdb=" O SER D 492 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE D 734 " --> pdb=" O PRO D 494 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 646 through 648 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) removed outlier: 8.951A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1207 hydrogen bonds defined for protein. 3525 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: 6.16 Time building geometry restraints manager: 2.99 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: 0.00 - 3.57: 37599 3.57 - 7.13: 307 7.13 - 10.70: 38 10.70 - 14.26: 8 14.26 - 17.83: 4 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: 6643 2.78 - 3.31: 25187 3.31 - 3.84: 46076 3.84 - 4.37: 55777 4.37 - 4.90: 89858 Nonbonded interactions: 223541 Sorted by model distance: nonbonded pdb=" OH TYR C 77 " pdb=" O PHE C 101 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR D 77 " pdb=" O PHE D 101 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR A 77 " pdb=" O PHE A 101 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR B 77 " pdb=" O PHE B 101 " model vdw 2.249 3.040 nonbonded pdb=" NH1 ARG A 485 " pdb=" OAA ZK1 A1301 " model vdw 2.289 3.120 ... (remaining 223536 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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: 2.020 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.940 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 28068 Z= 0.353 Angle : 0.930 17.830 37976 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 % Allowed : 1.15 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 485 TYR 0.018 0.002 TYR A1135 PHE 0.017 0.002 PHE D 133 TRP 0.026 0.003 TRP A 606 HIS 0.008 0.002 HIS C1181 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.35 (28058) covalent geometry : angle 0.93004 / 0.54 (37956) SS BOND : bond 0.00459 / 0.25 ( 10) SS BOND : angle 1.28395 / 0.91 ( 20) hydrogen bonds : bond 0.27449 / 18.09 ( 1207) hydrogen bonds : angle 10.14457 / 7.08 ( 3525) *********************** 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 to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9403 (t0) cc_final: 0.9162 (t70) REVERT: A 125 ILE cc_start: 0.9599 (mt) cc_final: 0.9337 (tt) REVERT: A 129 GLN cc_start: 0.9229 (mt0) cc_final: 0.8966 (pm20) REVERT: A 138 ASP cc_start: 0.8413 (t0) cc_final: 0.8190 (p0) REVERT: A 152 SER cc_start: 0.9275 (m) cc_final: 0.8996 (t) REVERT: A 193 ILE cc_start: 0.9598 (mt) cc_final: 0.9304 (mm) REVERT: A 196 CYS cc_start: 0.7895 (m) cc_final: 0.7342 (m) REVERT: A 221 ILE cc_start: 0.9324 (mt) cc_final: 0.9029 (mt) REVERT: A 427 ASP cc_start: 0.9111 (m-30) cc_final: 0.8700 (m-30) REVERT: A 431 GLU cc_start: 0.9369 (mm-30) cc_final: 0.8729 (tp30) REVERT: A 463 MET cc_start: 0.8616 (mtm) cc_final: 0.8391 (mtt) REVERT: A 479 LEU cc_start: 0.9283 (tp) cc_final: 0.8996 (tp) REVERT: A 503 MET cc_start: 0.9310 (ttm) cc_final: 0.8948 (ppp) REVERT: A 625 THR cc_start: 0.9529 (m) cc_final: 0.9307 (p) REVERT: A 634 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8463 (mm-30) REVERT: A 644 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8097 (tp30) REVERT: A 657 GLU cc_start: 0.9314 (tt0) cc_final: 0.8937 (tm-30) REVERT: A 661 ARG cc_start: 0.8953 (ttt180) cc_final: 0.8632 (tmt170) REVERT: A 669 LYS cc_start: 0.9703 (ttmt) cc_final: 0.9465 (ptmm) REVERT: A 670 MET cc_start: 0.9540 (mtp) cc_final: 0.9210 (mtt) REVERT: A 707 THR cc_start: 0.8725 (p) cc_final: 0.8232 (t) REVERT: A 710 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8574 (mt-10) REVERT: A 1198 ASP cc_start: 0.9258 (m-30) cc_final: 0.8807 (p0) outliers start: 2 outliers final: 0 residues processed: 224 average time/residue: 0.1000 time to fit residues: 29.4262 Evaluate side-chains 121 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.308 Evaluate side-chains 178 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ASN cc_start: 0.8869 (t0) cc_final: 0.8371 (p0) REVERT: B 116 ASP cc_start: 0.8787 (t0) cc_final: 0.8469 (t70) REVERT: B 131 ASP cc_start: 0.7917 (p0) cc_final: 0.7314 (p0) REVERT: B 167 ASN cc_start: 0.8596 (m-40) cc_final: 0.8024 (p0) REVERT: B 286 TYR cc_start: 0.7415 (t80) cc_final: 0.7125 (t80) REVERT: B 361 MET cc_start: 0.8264 (mmm) cc_final: 0.7833 (mmm) REVERT: B 425 CYS cc_start: 0.9617 (m) cc_final: 0.9337 (m) REVERT: B 480 THR cc_start: 0.9482 (m) cc_final: 0.9211 (p) REVERT: B 508 GLN cc_start: 0.9147 (tt0) cc_final: 0.8943 (mp10) REVERT: B 620 LEU cc_start: 0.9389 (tp) cc_final: 0.9140 (mt) REVERT: B 625 THR cc_start: 0.9295 (m) cc_final: 0.9052 (p) REVERT: B 707 THR cc_start: 0.9199 (p) cc_final: 0.8966 (p) REVERT: B 710 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8774 (tp30) REVERT: B 716 LYS cc_start: 0.9306 (mttt) cc_final: 0.9084 (mmmm) REVERT: B 762 LEU cc_start: 0.9423 (mt) cc_final: 0.9169 (tp) REVERT: B 792 VAL cc_start: 0.8649 (t) cc_final: 0.8373 (m) outliers start: 2 outliers final: 0 residues processed: 178 average time/residue: 0.1022 time to fit residues: 22.8242 Evaluate side-chains 86 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 0.0470 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.0070 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 overall best weight: 3.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A1016 ASN A1037 GLN A1092 HIS ** A1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1229 ASN B 65 GLN B 83 ASN B 112 GLN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN B 359 ASN B 392 GLN B 412 HIS B 714 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.072441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.057514 restraints weight = 46627.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.059135 restraints weight = 27751.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.060202 restraints weight = 19179.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.060981 restraints weight = 14712.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.061484 restraints weight = 12071.706| |-----------------------------------------------------------------------------| r_work (final): 0.3324 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.063722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.050000 restraints weight = 40269.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.051278 restraints weight = 26029.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.052186 restraints weight = 19199.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.052794 restraints weight = 15395.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.053309 restraints weight = 13141.489| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28068 Z= 0.199 Angle : 0.682 14.808 37976 Z= 0.369 Chirality : 0.044 0.227 4220 Planarity : 0.006 0.092 4756 Dihedral : 6.744 77.904 3786 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.87 % Favored : 94.96 % Rotamer: Outliers : 0.14 % Allowed : 3.04 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.13), residues: 3452 helix: -1.17 (0.11), residues: 1660 sheet: -2.37 (0.22), residues: 440 loop : -1.61 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 628 TYR 0.019 0.002 TYR B 177 PHE 0.021 0.002 PHE D 607 TRP 0.016 0.002 TRP A1208 HIS 0.004 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 (28058) covalent geometry : angle 0.68226 / 0.37 (37956) SS BOND : bond 0.00130 / 0.08 ( 10) SS BOND : angle 1.02955 / 0.65 ( 20) hydrogen bonds : bond 0.05090 / 3.30 ( 1207) hydrogen bonds : angle 6.10256 / 4.32 ( 3525) *********************** REFINEMENT MACRO_CYCLE 2 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 147 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.9738 (tt) cc_final: 0.9505 (pp) REVERT: A 138 ASP cc_start: 0.8093 (t0) cc_final: 0.7687 (p0) REVERT: A 152 SER cc_start: 0.9367 (m) cc_final: 0.9106 (t) REVERT: A 193 ILE cc_start: 0.9653 (mt) cc_final: 0.9335 (mm) REVERT: A 196 CYS cc_start: 0.7945 (m) cc_final: 0.7033 (m) REVERT: A 221 ILE cc_start: 0.9541 (mt) cc_final: 0.9176 (mt) REVERT: A 384 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7526 (pp20) REVERT: A 408 MET cc_start: 0.8729 (mmm) cc_final: 0.7949 (mmm) REVERT: A 427 ASP cc_start: 0.9079 (m-30) cc_final: 0.8716 (m-30) REVERT: A 442 LEU cc_start: 0.9327 (mt) cc_final: 0.9097 (mt) REVERT: A 456 ASP cc_start: 0.8962 (m-30) cc_final: 0.8456 (p0) REVERT: A 517 PHE cc_start: 0.7589 (t80) cc_final: 0.7284 (t80) REVERT: A 633 ILE cc_start: 0.9363 (mp) cc_final: 0.8876 (mp) REVERT: A 644 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7945 (tp30) REVERT: A 670 MET cc_start: 0.9418 (mtp) cc_final: 0.9145 (mtt) REVERT: A 705 GLU cc_start: 0.9141 (mp0) cc_final: 0.8863 (mp0) REVERT: A 707 THR cc_start: 0.9332 (p) cc_final: 0.8287 (t) REVERT: A 722 LYS cc_start: 0.8613 (tttt) cc_final: 0.8094 (ttmm) REVERT: A 746 VAL cc_start: 0.9537 (t) cc_final: 0.9319 (p) REVERT: A 1111 ARG cc_start: 0.8691 (ttm110) cc_final: 0.8299 (ptt-90) REVERT: A 1135 TYR cc_start: 0.8365 (t80) cc_final: 0.8111 (t80) REVERT: A 1184 TYR cc_start: 0.8775 (t80) cc_final: 0.8445 (t80) REVERT: A 1198 ASP cc_start: 0.9333 (m-30) cc_final: 0.8863 (p0) REVERT: A 1228 LEU cc_start: 0.9332 (mt) cc_final: 0.9101 (mt) outliers start: 2 outliers final: 1 residues processed: 145 average time/residue: 0.0897 time to fit residues: 17.6524 Evaluate side-chains 106 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.295 Evaluate side-chains 94 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: D 54 ASN cc_start: 0.8957 (t0) cc_final: 0.8597 (p0) REVERT: D 361 MET cc_start: 0.8193 (mmm) cc_final: 0.7892 (mmm) REVERT: D 408 MET cc_start: 0.7894 (mmm) cc_final: 0.7558 (mmm) REVERT: D 425 CYS cc_start: 0.9585 (m) cc_final: 0.9259 (m) REVERT: D 503 MET cc_start: 0.9035 (ptm) cc_final: 0.8536 (ptp) REVERT: D 517 PHE cc_start: 0.7941 (t80) cc_final: 0.7436 (t80) REVERT: D 704 LEU cc_start: 0.9132 (tp) cc_final: 0.8418 (tt) REVERT: D 710 GLU cc_start: 0.9473 (mt-10) cc_final: 0.8977 (tp30) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0637 time to fit residues: 8.6224 Evaluate side-chains 61 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 209 optimal weight: 7.9990 chunk 339 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 169 optimal weight: 0.8980 chunk 140 optimal weight: 0.2980 chunk 181 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 119 optimal weight: 0.0050 chunk 147 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 HIS A1016 ASN A1092 HIS A1181 HIS A1229 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 335 GLN D 359 ASN D 392 GLN D 412 HIS ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.073254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.057412 restraints weight = 45160.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.059018 restraints weight = 26798.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.060136 restraints weight = 18588.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.060921 restraints weight = 14240.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.061436 restraints weight = 11710.661| |-----------------------------------------------------------------------------| r_work (final): 0.3311 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.064859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.050888 restraints weight = 39357.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.052249 restraints weight = 25360.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.053190 restraints weight = 18444.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.053869 restraints weight = 14694.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.054409 restraints weight = 12399.231| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28068 Z= 0.125 Angle : 0.603 13.984 37976 Z= 0.319 Chirality : 0.043 0.227 4220 Planarity : 0.005 0.085 4756 Dihedral : 6.198 69.545 3786 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.69 % Favored : 95.13 % Rotamer: Outliers : 0.14 % Allowed : 3.11 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.13), residues: 3452 helix: -0.29 (0.12), residues: 1646 sheet: -2.18 (0.22), residues: 428 loop : -1.48 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 660 TYR 0.020 0.001 TYR A1206 PHE 0.020 0.001 PHE C1210 TRP 0.019 0.002 TRP A1208 HIS 0.002 0.000 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (28058) covalent geometry : angle 0.60244 / 0.32 (37956) SS BOND : bond 0.00211 / 0.12 ( 10) SS BOND : angle 0.96955 / 0.63 ( 20) hydrogen bonds : bond 0.04020 / 2.60 ( 1207) hydrogen bonds : angle 5.38177 / 3.84 ( 3525) *********************** REFINEMENT MACRO_CYCLE 3 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 141 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.308 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: C 78 ASP cc_start: 0.9228 (t70) cc_final: 0.8850 (p0) REVERT: C 129 GLN cc_start: 0.8990 (mt0) cc_final: 0.8774 (pm20) REVERT: C 152 SER cc_start: 0.9335 (m) cc_final: 0.9069 (t) REVERT: C 196 CYS cc_start: 0.7859 (m) cc_final: 0.6759 (m) REVERT: C 221 ILE cc_start: 0.9593 (mt) cc_final: 0.9296 (mm) REVERT: C 232 LEU cc_start: 0.8385 (pt) cc_final: 0.8111 (mp) REVERT: C 408 MET cc_start: 0.8818 (mmm) cc_final: 0.8184 (mmm) REVERT: C 424 TYR cc_start: 0.9143 (t80) cc_final: 0.8605 (t80) REVERT: C 427 ASP cc_start: 0.9066 (m-30) cc_final: 0.8598 (m-30) REVERT: C 474 ILE cc_start: 0.9224 (tt) cc_final: 0.8933 (mt) REVERT: C 479 LEU cc_start: 0.9291 (tp) cc_final: 0.8822 (tp) REVERT: C 486 GLU cc_start: 0.8363 (tt0) cc_final: 0.7753 (tm-30) REVERT: C 491 PHE cc_start: 0.8590 (m-10) cc_final: 0.8211 (m-10) REVERT: C 503 MET cc_start: 0.9088 (ptm) cc_final: 0.8710 (ppp) REVERT: C 526 TRP cc_start: 0.7209 (m100) cc_final: 0.6377 (m100) REVERT: C 527 MET cc_start: 0.7405 (mtm) cc_final: 0.6605 (ttt) REVERT: C 644 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8051 (tp30) REVERT: C 705 GLU cc_start: 0.9203 (mp0) cc_final: 0.8889 (mp0) REVERT: C 707 THR cc_start: 0.9347 (p) cc_final: 0.8679 (t) REVERT: C 708 MET cc_start: 0.9022 (tpt) cc_final: 0.8805 (tpt) REVERT: C 746 VAL cc_start: 0.9519 (t) cc_final: 0.9249 (p) REVERT: C 1184 TYR cc_start: 0.8587 (t80) cc_final: 0.8312 (t80) REVERT: C 1198 ASP cc_start: 0.9153 (m-30) cc_final: 0.8787 (p0) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.0770 time to fit residues: 15.2673 Evaluate side-chains 101 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.224 Evaluate side-chains 95 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: D 54 ASN cc_start: 0.8997 (t0) cc_final: 0.8630 (p0) REVERT: D 131 ASP cc_start: 0.7896 (p0) cc_final: 0.7015 (t0) REVERT: D 194 LEU cc_start: 0.9502 (tt) cc_final: 0.9193 (tt) REVERT: D 359 ASN cc_start: 0.9321 (m-40) cc_final: 0.8591 (m-40) REVERT: D 361 MET cc_start: 0.8144 (mmm) cc_final: 0.7748 (mmm) REVERT: D 425 CYS cc_start: 0.9569 (m) cc_final: 0.9222 (m) REVERT: D 463 MET cc_start: 0.8998 (ptp) cc_final: 0.8696 (ptp) REVERT: D 503 MET cc_start: 0.8880 (ptm) cc_final: 0.8413 (ptp) REVERT: D 517 PHE cc_start: 0.7773 (t80) cc_final: 0.7465 (t80) REVERT: D 629 MET cc_start: 0.7673 (mmt) cc_final: 0.7180 (mmt) REVERT: D 633 ILE cc_start: 0.9140 (mm) cc_final: 0.8895 (mp) REVERT: D 704 LEU cc_start: 0.9122 (tp) cc_final: 0.8441 (tt) REVERT: D 710 GLU cc_start: 0.9409 (mt-10) cc_final: 0.8892 (tt0) REVERT: D 730 LYS cc_start: 0.8428 (mmpt) cc_final: 0.8215 (mmmm) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.0698 time to fit residues: 9.1876 Evaluate side-chains 67 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 162 optimal weight: 0.3980 chunk 163 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 301 optimal weight: 6.9990 chunk 337 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 186 optimal weight: 0.7980 chunk 156 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 341 optimal weight: 0.0000 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 147 GLN C 214 HIS C 586 GLN C 619 ASN C1016 ASN C1229 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 167 ASN D 214 HIS D 219 HIS D 311 ASN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.070882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.055237 restraints weight = 47087.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.056853 restraints weight = 27692.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.057972 restraints weight = 19126.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058724 restraints weight = 14614.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.059264 restraints weight = 12007.296| |-----------------------------------------------------------------------------| r_work (final): 0.3264 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.062400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.048756 restraints weight = 41174.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.050017 restraints weight = 26402.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.050932 restraints weight = 19389.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.051570 restraints weight = 15480.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.051866 restraints weight = 13186.629| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28068 Z= 0.155 Angle : 0.607 13.035 37976 Z= 0.322 Chirality : 0.042 0.176 4220 Planarity : 0.004 0.053 4756 Dihedral : 5.895 64.156 3786 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.39 % Favored : 94.44 % Rotamer: Outliers : 0.07 % Allowed : 2.30 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3452 helix: 0.23 (0.12), residues: 1634 sheet: -1.91 (0.22), residues: 460 loop : -1.24 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 660 TYR 0.014 0.001 TYR C 711 PHE 0.017 0.001 PHE C 584 TRP 0.019 0.002 TRP A1199 HIS 0.005 0.001 HIS A1202 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (28058) covalent geometry : angle 0.60656 / 0.32 (37956) SS BOND : bond 0.00148 / 0.10 ( 10) SS BOND : angle 0.76196 / 0.50 ( 20) hydrogen bonds : bond 0.03688 / 2.40 ( 1207) hydrogen bonds : angle 5.22463 / 3.73 ( 3525) *********************** REFINEMENT MACRO_CYCLE 4 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 122 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 SER cc_start: 0.9366 (m) cc_final: 0.9049 (p) REVERT: A 190 ARG cc_start: 0.7993 (mmt-90) cc_final: 0.7600 (mmt-90) REVERT: A 221 ILE cc_start: 0.9574 (mt) cc_final: 0.9302 (mm) REVERT: A 232 LEU cc_start: 0.8740 (pt) cc_final: 0.8431 (mp) REVERT: A 380 MET cc_start: 0.8787 (mmm) cc_final: 0.8505 (ttm) REVERT: A 384 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7357 (tm-30) REVERT: A 408 MET cc_start: 0.8696 (mmm) cc_final: 0.7954 (mmm) REVERT: A 427 ASP cc_start: 0.9109 (m-30) cc_final: 0.8676 (m-30) REVERT: A 486 GLU cc_start: 0.8561 (tt0) cc_final: 0.7952 (tm-30) REVERT: A 503 MET cc_start: 0.9214 (ptm) cc_final: 0.8409 (ppp) REVERT: A 526 TRP cc_start: 0.7422 (m100) cc_final: 0.6682 (m100) REVERT: A 644 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7635 (tp30) REVERT: A 670 MET cc_start: 0.9199 (mtm) cc_final: 0.8914 (mtm) REVERT: A 708 MET cc_start: 0.9079 (tpt) cc_final: 0.8741 (tpt) REVERT: A 721 MET cc_start: 0.8431 (ptp) cc_final: 0.8217 (ptm) REVERT: A 722 LYS cc_start: 0.8909 (tttt) cc_final: 0.7422 (tttt) REVERT: A 1021 LEU cc_start: 0.7910 (mt) cc_final: 0.7709 (tp) REVERT: A 1025 THR cc_start: 0.8384 (m) cc_final: 0.8059 (p) REVERT: A 1184 TYR cc_start: 0.8857 (t80) cc_final: 0.8460 (t80) REVERT: A 1198 ASP cc_start: 0.9184 (m-30) cc_final: 0.8849 (p0) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0788 time to fit residues: 13.6885 Evaluate side-chains 89 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.275 Evaluate side-chains 74 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 54 ASN cc_start: 0.9039 (t0) cc_final: 0.8733 (p0) REVERT: D 88 PHE cc_start: 0.8426 (m-10) cc_final: 0.8153 (m-10) REVERT: D 359 ASN cc_start: 0.9270 (m-40) cc_final: 0.8477 (m-40) REVERT: D 361 MET cc_start: 0.8154 (mmm) cc_final: 0.7816 (mmm) REVERT: D 425 CYS cc_start: 0.9586 (m) cc_final: 0.9305 (m) REVERT: D 491 PHE cc_start: 0.7288 (m-80) cc_final: 0.7079 (m-10) REVERT: D 503 MET cc_start: 0.8834 (ptm) cc_final: 0.8422 (ptp) REVERT: D 517 PHE cc_start: 0.7901 (t80) cc_final: 0.7594 (t80) REVERT: D 633 ILE cc_start: 0.9210 (mm) cc_final: 0.8994 (mp) REVERT: D 670 MET cc_start: 0.9396 (ptp) cc_final: 0.9081 (ptp) REVERT: D 710 GLU cc_start: 0.9418 (mt-10) cc_final: 0.8935 (tt0) REVERT: D 808 LEU cc_start: 0.8976 (tp) cc_final: 0.8768 (mp) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.0631 time to fit residues: 6.7815 Evaluate side-chains 55 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 100 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 282 optimal weight: 0.9990 chunk 263 optimal weight: 8.9990 chunk 267 optimal weight: 9.9990 chunk 321 optimal weight: 0.9980 chunk 280 optimal weight: 0.0060 chunk 236 optimal weight: 7.9990 chunk 322 optimal weight: 6.9990 chunk 206 optimal weight: 0.7980 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 HIS A1016 ASN A1181 HIS A1229 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN D 642 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.071095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.055433 restraints weight = 46530.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.057018 restraints weight = 27317.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.058127 restraints weight = 18878.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.058911 restraints weight = 14459.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.059379 restraints weight = 11864.687| |-----------------------------------------------------------------------------| r_work (final): 0.3262 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.063371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.049602 restraints weight = 40230.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.050885 restraints weight = 25825.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.051795 restraints weight = 18915.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.052412 restraints weight = 15147.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.052900 restraints weight = 12916.931| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28068 Z= 0.118 Angle : 0.566 13.088 37976 Z= 0.300 Chirality : 0.042 0.213 4220 Planarity : 0.004 0.099 4756 Dihedral : 5.710 62.278 3786 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.98 % Favored : 94.84 % Rotamer: Outliers : 0.07 % Allowed : 2.30 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.14), residues: 3452 helix: 0.52 (0.13), residues: 1664 sheet: -1.91 (0.23), residues: 432 loop : -1.15 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 628 TYR 0.016 0.001 TYR A1135 PHE 0.025 0.001 PHE A1210 TRP 0.021 0.002 TRP C1199 HIS 0.005 0.001 HIS C1181 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (28058) covalent geometry : angle 0.56613 / 0.30 (37956) SS BOND : bond 0.00105 / 0.07 ( 10) SS BOND : angle 0.73518 / 0.48 ( 20) hydrogen bonds : bond 0.03491 / 2.27 ( 1207) hydrogen bonds : angle 4.96424 / 3.56 ( 3525) *********************** REFINEMENT MACRO_CYCLE 5 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 115 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 ASP cc_start: 0.9257 (t70) cc_final: 0.8943 (p0) REVERT: C 152 SER cc_start: 0.9482 (m) cc_final: 0.9199 (p) REVERT: C 232 LEU cc_start: 0.8628 (pt) cc_final: 0.8318 (mp) REVERT: C 249 ASP cc_start: 0.7286 (t0) cc_final: 0.7047 (t0) REVERT: C 358 ILE cc_start: 0.9377 (mt) cc_final: 0.9101 (mp) REVERT: C 384 GLU cc_start: 0.8502 (mt-10) cc_final: 0.7446 (tm-30) REVERT: C 408 MET cc_start: 0.8826 (mmm) cc_final: 0.8202 (mmm) REVERT: C 424 TYR cc_start: 0.9200 (t80) cc_final: 0.8700 (t80) REVERT: C 427 ASP cc_start: 0.9135 (m-30) cc_final: 0.8640 (m-30) REVERT: C 486 GLU cc_start: 0.8362 (tt0) cc_final: 0.7894 (tm-30) REVERT: C 503 MET cc_start: 0.9230 (ptm) cc_final: 0.8586 (ppp) REVERT: C 526 TRP cc_start: 0.7519 (m100) cc_final: 0.6437 (m100) REVERT: C 527 MET cc_start: 0.6850 (ttt) cc_final: 0.6525 (ttt) REVERT: C 644 GLU cc_start: 0.8508 (mt-10) cc_final: 0.7782 (tp30) REVERT: C 699 LYS cc_start: 0.9661 (tppt) cc_final: 0.9275 (tppt) REVERT: C 705 GLU cc_start: 0.9210 (mp0) cc_final: 0.8956 (mp0) REVERT: C 707 THR cc_start: 0.9393 (p) cc_final: 0.8690 (t) REVERT: C 708 MET cc_start: 0.9159 (tpt) cc_final: 0.8819 (tpt) REVERT: C 710 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8932 (pt0) REVERT: C 1021 LEU cc_start: 0.7968 (mt) cc_final: 0.7753 (tp) REVERT: C 1032 TRP cc_start: 0.7825 (t-100) cc_final: 0.7603 (t-100) REVERT: C 1184 TYR cc_start: 0.8658 (t80) cc_final: 0.8090 (t80) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0701 time to fit residues: 11.8743 Evaluate side-chains 90 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.391 Evaluate side-chains 76 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 54 ASN cc_start: 0.9059 (t0) cc_final: 0.8725 (p0) REVERT: D 88 PHE cc_start: 0.8348 (m-10) cc_final: 0.8093 (m-10) REVERT: D 358 ILE cc_start: 0.9373 (mt) cc_final: 0.9164 (mt) REVERT: D 359 ASN cc_start: 0.9311 (m-40) cc_final: 0.8310 (m-40) REVERT: D 361 MET cc_start: 0.8204 (mmm) cc_final: 0.7840 (mmm) REVERT: D 407 MET cc_start: 0.8083 (mmm) cc_final: 0.7871 (mmm) REVERT: D 425 CYS cc_start: 0.9551 (m) cc_final: 0.9252 (m) REVERT: D 463 MET cc_start: 0.8917 (ptp) cc_final: 0.8384 (ppp) REVERT: D 491 PHE cc_start: 0.7278 (m-80) cc_final: 0.7065 (m-10) REVERT: D 503 MET cc_start: 0.8762 (ptm) cc_final: 0.8375 (ptp) REVERT: D 517 PHE cc_start: 0.8055 (t80) cc_final: 0.7741 (t80) REVERT: D 670 MET cc_start: 0.9391 (ptp) cc_final: 0.9179 (ptp) REVERT: D 710 GLU cc_start: 0.9419 (mt-10) cc_final: 0.8958 (tt0) REVERT: D 808 LEU cc_start: 0.8998 (tp) cc_final: 0.8781 (mp) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.0655 time to fit residues: 7.1686 Evaluate side-chains 56 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 107 optimal weight: 0.3980 chunk 72 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 327 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 147 GLN C 214 HIS C 586 GLN C 619 ASN C1016 ASN C1181 HIS C1229 ASN D 112 GLN D 246 GLN ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.071525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.056000 restraints weight = 46008.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.057639 restraints weight = 26999.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.058755 restraints weight = 18562.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.059549 restraints weight = 14175.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.060105 restraints weight = 11622.463| |-----------------------------------------------------------------------------| r_work (final): 0.3287 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.064196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.050431 restraints weight = 40204.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.051714 restraints weight = 26204.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.052634 restraints weight = 19303.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.053252 restraints weight = 15427.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.053593 restraints weight = 13177.927| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28068 Z= 0.107 Angle : 0.560 12.398 37976 Z= 0.293 Chirality : 0.042 0.202 4220 Planarity : 0.004 0.047 4756 Dihedral : 5.493 62.535 3786 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.69 % Favored : 95.19 % Rotamer: Outliers : 0.07 % Allowed : 2.10 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3452 helix: 0.81 (0.13), residues: 1642 sheet: -1.78 (0.23), residues: 440 loop : -1.11 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 628 TYR 0.016 0.001 TYR A1135 PHE 0.015 0.001 PHE C 623 TRP 0.025 0.002 TRP A1199 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (28058) covalent geometry : angle 0.56009 / 0.29 (37956) SS BOND : bond 0.00088 / 0.06 ( 10) SS BOND : angle 0.72116 / 0.46 ( 20) hydrogen bonds : bond 0.03133 / 2.05 ( 1207) hydrogen bonds : angle 4.76967 / 3.41 ( 3525) *********************** REFINEMENT MACRO_CYCLE 6 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 116 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 ASP cc_start: 0.9246 (t70) cc_final: 0.8890 (p0) REVERT: C 152 SER cc_start: 0.9447 (m) cc_final: 0.9172 (p) REVERT: C 232 LEU cc_start: 0.8625 (pt) cc_final: 0.8304 (mp) REVERT: C 249 ASP cc_start: 0.7380 (t0) cc_final: 0.7100 (t0) REVERT: C 358 ILE cc_start: 0.9376 (mt) cc_final: 0.9104 (mp) REVERT: C 380 MET cc_start: 0.8593 (mmm) cc_final: 0.8311 (mmm) REVERT: C 384 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7436 (tm-30) REVERT: C 408 MET cc_start: 0.8792 (mmm) cc_final: 0.8135 (mmm) REVERT: C 424 TYR cc_start: 0.9155 (t80) cc_final: 0.8665 (t80) REVERT: C 427 ASP cc_start: 0.9131 (m-30) cc_final: 0.8672 (m-30) REVERT: C 486 GLU cc_start: 0.8427 (tt0) cc_final: 0.7958 (tm-30) REVERT: C 503 MET cc_start: 0.9211 (ptm) cc_final: 0.8582 (ppp) REVERT: C 526 TRP cc_start: 0.7564 (m100) cc_final: 0.6715 (m100) REVERT: C 527 MET cc_start: 0.6782 (ttt) cc_final: 0.6582 (ttt) REVERT: C 644 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7670 (tp30) REVERT: C 699 LYS cc_start: 0.9658 (tppt) cc_final: 0.9297 (tppt) REVERT: C 705 GLU cc_start: 0.9160 (mp0) cc_final: 0.8931 (mp0) REVERT: C 707 THR cc_start: 0.9493 (p) cc_final: 0.8638 (t) REVERT: C 708 MET cc_start: 0.9198 (tpt) cc_final: 0.8828 (tpt) REVERT: C 710 GLU cc_start: 0.9305 (mm-30) cc_final: 0.8938 (pt0) REVERT: C 722 LYS cc_start: 0.8376 (tttt) cc_final: 0.8129 (mtpt) REVERT: C 1025 THR cc_start: 0.8329 (m) cc_final: 0.8020 (p) REVERT: C 1184 TYR cc_start: 0.8635 (t80) cc_final: 0.8393 (t80) REVERT: C 1214 TRP cc_start: 0.8354 (m-10) cc_final: 0.8118 (m-10) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0823 time to fit residues: 13.4861 Evaluate side-chains 94 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.301 Evaluate side-chains 76 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: D 54 ASN cc_start: 0.9050 (t0) cc_final: 0.8717 (p0) REVERT: D 88 PHE cc_start: 0.8267 (m-10) cc_final: 0.7964 (m-10) REVERT: D 358 ILE cc_start: 0.9327 (mt) cc_final: 0.9120 (mt) REVERT: D 359 ASN cc_start: 0.9208 (m-40) cc_final: 0.8395 (m-40) REVERT: D 425 CYS cc_start: 0.9520 (m) cc_final: 0.9290 (m) REVERT: D 463 MET cc_start: 0.8930 (ptp) cc_final: 0.8374 (ppp) REVERT: D 491 PHE cc_start: 0.7320 (m-80) cc_final: 0.7090 (m-10) REVERT: D 503 MET cc_start: 0.8719 (ptm) cc_final: 0.8415 (ptp) REVERT: D 517 PHE cc_start: 0.8004 (t80) cc_final: 0.7689 (t80) REVERT: D 710 GLU cc_start: 0.9388 (mt-10) cc_final: 0.8895 (tt0) REVERT: D 808 LEU cc_start: 0.9056 (tp) cc_final: 0.8848 (mp) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.0671 time to fit residues: 7.2515 Evaluate side-chains 55 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 160 optimal weight: 0.9990 chunk 283 optimal weight: 0.0010 chunk 90 optimal weight: 10.0000 chunk 186 optimal weight: 0.0770 chunk 91 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 166 optimal weight: 0.0000 chunk 271 optimal weight: 10.0000 chunk 335 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 619 ASN C1181 HIS C1229 ASN D 112 GLN D 435 HIS ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.072201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.056428 restraints weight = 45690.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.058062 restraints weight = 26874.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.059178 restraints weight = 18593.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.059961 restraints weight = 14208.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.060463 restraints weight = 11681.410| |-----------------------------------------------------------------------------| r_work (final): 0.3296 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.064888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.051333 restraints weight = 39875.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.052592 restraints weight = 25961.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.053513 restraints weight = 19267.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.054137 restraints weight = 15422.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.054610 restraints weight = 13161.137| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28068 Z= 0.105 Angle : 0.576 13.192 37976 Z= 0.298 Chirality : 0.043 0.220 4220 Planarity : 0.004 0.062 4756 Dihedral : 5.466 60.654 3786 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 0.07 % Allowed : 0.95 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3452 helix: 0.99 (0.13), residues: 1640 sheet: -1.78 (0.23), residues: 440 loop : -1.07 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 628 TYR 0.016 0.001 TYR A1135 PHE 0.031 0.001 PHE D 623 TRP 0.042 0.002 TRP A 323 HIS 0.003 0.000 HIS C1181 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (28058) covalent geometry : angle 0.57587 / 0.30 (37956) SS BOND : bond 0.00119 / 0.07 ( 10) SS BOND : angle 0.81399 / 0.56 ( 20) hydrogen bonds : bond 0.03115 / 2.06 ( 1207) hydrogen bonds : angle 4.63454 / 3.32 ( 3525) *********************** REFINEMENT MACRO_CYCLE 7 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 116 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 ASP cc_start: 0.9186 (t70) cc_final: 0.8874 (p0) REVERT: C 152 SER cc_start: 0.9488 (m) cc_final: 0.9223 (p) REVERT: C 232 LEU cc_start: 0.8641 (pt) cc_final: 0.8345 (mm) REVERT: C 249 ASP cc_start: 0.7254 (t0) cc_final: 0.6988 (t0) REVERT: C 292 MET cc_start: 0.8772 (tmm) cc_final: 0.8556 (tmm) REVERT: C 358 ILE cc_start: 0.9348 (mt) cc_final: 0.9075 (mp) REVERT: C 380 MET cc_start: 0.8689 (mmm) cc_final: 0.8430 (mmm) REVERT: C 384 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7511 (tm-30) REVERT: C 408 MET cc_start: 0.8808 (mmm) cc_final: 0.8146 (mmm) REVERT: C 424 TYR cc_start: 0.9054 (t80) cc_final: 0.8530 (t80) REVERT: C 427 ASP cc_start: 0.9108 (m-30) cc_final: 0.8585 (m-30) REVERT: C 486 GLU cc_start: 0.8516 (tt0) cc_final: 0.8145 (tm-30) REVERT: C 503 MET cc_start: 0.9225 (ptm) cc_final: 0.8527 (ppp) REVERT: C 526 TRP cc_start: 0.7575 (m100) cc_final: 0.6846 (m100) REVERT: C 644 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7881 (tp30) REVERT: C 705 GLU cc_start: 0.9152 (mp0) cc_final: 0.8879 (mp0) REVERT: C 707 THR cc_start: 0.9436 (p) cc_final: 0.9058 (t) REVERT: C 708 MET cc_start: 0.9165 (tpt) cc_final: 0.8865 (tpt) REVERT: C 710 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8881 (tp30) REVERT: C 722 LYS cc_start: 0.8352 (tttt) cc_final: 0.8009 (mtpt) REVERT: C 1169 PHE cc_start: 0.8844 (m-80) cc_final: 0.8513 (m-80) REVERT: C 1184 TYR cc_start: 0.8622 (t80) cc_final: 0.8124 (t80) REVERT: C 1214 TRP cc_start: 0.8263 (m-10) cc_final: 0.7927 (m-10) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0729 time to fit residues: 12.3193 Evaluate side-chains 90 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.326 Evaluate side-chains 75 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 54 ASN cc_start: 0.9086 (t0) cc_final: 0.8735 (p0) REVERT: D 88 PHE cc_start: 0.8300 (m-10) cc_final: 0.7988 (m-10) REVERT: D 358 ILE cc_start: 0.9348 (mt) cc_final: 0.9068 (mm) REVERT: D 359 ASN cc_start: 0.9175 (m-40) cc_final: 0.8525 (m-40) REVERT: D 425 CYS cc_start: 0.9525 (m) cc_final: 0.9268 (m) REVERT: D 463 MET cc_start: 0.8912 (ptp) cc_final: 0.8340 (ppp) REVERT: D 503 MET cc_start: 0.8722 (ptm) cc_final: 0.8446 (ptp) REVERT: D 517 PHE cc_start: 0.8100 (t80) cc_final: 0.7796 (t80) REVERT: D 710 GLU cc_start: 0.9411 (mt-10) cc_final: 0.8897 (tt0) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.0647 time to fit residues: 6.9755 Evaluate side-chains 55 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 58 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 chunk 315 optimal weight: 0.2980 chunk 114 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 142 optimal weight: 0.0010 overall best weight: 1.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 619 ASN C1181 HIS C1229 ASN D 112 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.071760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056247 restraints weight = 45218.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.057820 restraints weight = 27077.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.058935 restraints weight = 18714.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.059706 restraints weight = 14274.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.060185 restraints weight = 11747.937| |-----------------------------------------------------------------------------| r_work (final): 0.3289 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.064539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.050964 restraints weight = 40146.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.052228 restraints weight = 26096.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.053105 restraints weight = 19306.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.053789 restraints weight = 15569.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.054204 restraints weight = 13221.879| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28068 Z= 0.110 Angle : 0.562 12.136 37976 Z= 0.292 Chirality : 0.042 0.222 4220 Planarity : 0.004 0.049 4756 Dihedral : 5.343 60.187 3786 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.75 % Favored : 95.19 % Rotamer: Outliers : 0.07 % Allowed : 0.74 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 3452 helix: 1.05 (0.13), residues: 1652 sheet: -1.82 (0.23), residues: 446 loop : -1.04 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 628 TYR 0.017 0.001 TYR A1184 PHE 0.037 0.001 PHE C1210 TRP 0.030 0.002 TRP C 323 HIS 0.007 0.001 HIS A1181 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (28058) covalent geometry : angle 0.56235 / 0.29 (37956) SS BOND : bond 0.00127 / 0.07 ( 10) SS BOND : angle 0.68099 / 0.46 ( 20) hydrogen bonds : bond 0.03046 / 2.01 ( 1207) hydrogen bonds : angle 4.59429 / 3.28 ( 3525) *********************** REFINEMENT MACRO_CYCLE 8 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 112 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 ASP cc_start: 0.9196 (t70) cc_final: 0.8922 (p0) REVERT: C 152 SER cc_start: 0.9497 (m) cc_final: 0.9235 (p) REVERT: C 232 LEU cc_start: 0.8631 (pt) cc_final: 0.8342 (mm) REVERT: C 249 ASP cc_start: 0.7095 (t0) cc_final: 0.6889 (t0) REVERT: C 292 MET cc_start: 0.8779 (tmm) cc_final: 0.8549 (tmm) REVERT: C 358 ILE cc_start: 0.9358 (mt) cc_final: 0.9082 (mp) REVERT: C 380 MET cc_start: 0.8754 (mmm) cc_final: 0.8480 (mmm) REVERT: C 384 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7507 (tm-30) REVERT: C 408 MET cc_start: 0.8829 (mmm) cc_final: 0.8177 (mmm) REVERT: C 424 TYR cc_start: 0.9048 (t80) cc_final: 0.8533 (t80) REVERT: C 427 ASP cc_start: 0.9116 (m-30) cc_final: 0.8639 (m-30) REVERT: C 486 GLU cc_start: 0.8528 (tt0) cc_final: 0.8191 (tm-30) REVERT: C 503 MET cc_start: 0.9229 (ptm) cc_final: 0.8559 (ppp) REVERT: C 526 TRP cc_start: 0.7674 (m100) cc_final: 0.6904 (m100) REVERT: C 644 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7795 (tp30) REVERT: C 705 GLU cc_start: 0.9150 (mp0) cc_final: 0.8923 (mp0) REVERT: C 707 THR cc_start: 0.9451 (p) cc_final: 0.9066 (t) REVERT: C 708 MET cc_start: 0.9173 (tpt) cc_final: 0.8863 (tpt) REVERT: C 710 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8887 (mm-30) REVERT: C 722 LYS cc_start: 0.8283 (tttt) cc_final: 0.7348 (tttt) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0686 time to fit residues: 11.4807 Evaluate side-chains 87 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.294 Evaluate side-chains 65 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 54 ASN cc_start: 0.9043 (t0) cc_final: 0.8804 (p0) REVERT: D 358 ILE cc_start: 0.9319 (mt) cc_final: 0.9068 (mm) REVERT: D 359 ASN cc_start: 0.9031 (m-40) cc_final: 0.8413 (m-40) REVERT: D 425 CYS cc_start: 0.9477 (m) cc_final: 0.9177 (m) REVERT: D 503 MET cc_start: 0.8707 (ptm) cc_final: 0.8475 (ptp) REVERT: D 517 PHE cc_start: 0.7925 (t80) cc_final: 0.7677 (t80) REVERT: D 629 MET cc_start: 0.7585 (ttm) cc_final: 0.7152 (ttm) REVERT: D 710 GLU cc_start: 0.9465 (mt-10) cc_final: 0.8945 (tt0) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.0618 time to fit residues: 5.9920 Evaluate side-chains 49 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 165 optimal weight: 0.2980 chunk 185 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 307 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 326 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 303 optimal weight: 8.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN C1181 HIS C1229 ASN D 112 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.069759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.054394 restraints weight = 47293.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.055927 restraints weight = 28050.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.056991 restraints weight = 19493.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.057731 restraints weight = 15020.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.058158 restraints weight = 12418.145| |-----------------------------------------------------------------------------| r_work (final): 0.3235 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.062952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.049523 restraints weight = 40564.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.050756 restraints weight = 26500.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.051583 restraints weight = 19578.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.052238 restraints weight = 15794.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.052731 restraints weight = 13457.349| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.6726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28068 Z= 0.145 Angle : 0.576 11.475 37976 Z= 0.306 Chirality : 0.042 0.210 4220 Planarity : 0.004 0.048 4756 Dihedral : 5.349 61.639 3786 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.16 % Favored : 94.79 % Rotamer: Outliers : 0.07 % Allowed : 0.68 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.15), residues: 3452 helix: 1.10 (0.13), residues: 1658 sheet: -1.81 (0.23), residues: 456 loop : -1.07 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 628 TYR 0.016 0.001 TYR A1135 PHE 0.022 0.001 PHE A1113 TRP 0.028 0.002 TRP A 323 HIS 0.005 0.001 HIS A1181 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (28058) covalent geometry : angle 0.57630 / 0.31 (37956) SS BOND : bond 0.00119 / 0.07 ( 10) SS BOND : angle 0.77573 / 0.51 ( 20) hydrogen bonds : bond 0.03135 / 2.06 ( 1207) hydrogen bonds : angle 4.71997 / 3.38 ( 3525) *********************** REFINEMENT MACRO_CYCLE 9 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 108 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 SER cc_start: 0.9529 (m) cc_final: 0.9277 (p) REVERT: C 232 LEU cc_start: 0.8613 (pt) cc_final: 0.8308 (mm) REVERT: C 292 MET cc_start: 0.8819 (tmm) cc_final: 0.8592 (tmm) REVERT: C 358 ILE cc_start: 0.9393 (mt) cc_final: 0.9118 (mp) REVERT: C 384 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7484 (tm-30) REVERT: C 408 MET cc_start: 0.8806 (mmm) cc_final: 0.8150 (mmm) REVERT: C 424 TYR cc_start: 0.9069 (t80) cc_final: 0.8576 (t80) REVERT: C 427 ASP cc_start: 0.9183 (m-30) cc_final: 0.8729 (m-30) REVERT: C 486 GLU cc_start: 0.8576 (tt0) cc_final: 0.8215 (tm-30) REVERT: C 503 MET cc_start: 0.9244 (ptm) cc_final: 0.8626 (ppp) REVERT: C 526 TRP cc_start: 0.7932 (m100) cc_final: 0.7048 (m100) REVERT: C 612 ILE cc_start: 0.9477 (mt) cc_final: 0.9234 (mt) REVERT: C 629 MET cc_start: 0.9217 (tpp) cc_final: 0.8847 (tmm) REVERT: C 644 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7593 (tp30) REVERT: C 705 GLU cc_start: 0.9166 (mp0) cc_final: 0.8936 (mp0) REVERT: C 707 THR cc_start: 0.9480 (p) cc_final: 0.9110 (t) REVERT: C 708 MET cc_start: 0.9179 (tpt) cc_final: 0.8850 (tpt) REVERT: C 710 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8870 (mm-30) REVERT: C 722 LYS cc_start: 0.8279 (tttt) cc_final: 0.7303 (tttt) REVERT: C 1032 TRP cc_start: 0.8431 (t-100) cc_final: 0.7330 (t60) REVERT: C 1184 TYR cc_start: 0.8710 (t80) cc_final: 0.8167 (t80) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0757 time to fit residues: 11.9813 Evaluate side-chains 86 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.301 Evaluate side-chains 64 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 54 ASN cc_start: 0.9032 (t0) cc_final: 0.8817 (p0) REVERT: D 425 CYS cc_start: 0.9471 (m) cc_final: 0.9190 (m) REVERT: D 503 MET cc_start: 0.8664 (ptm) cc_final: 0.8455 (ptp) REVERT: D 517 PHE cc_start: 0.8122 (t80) cc_final: 0.7830 (t80) REVERT: D 629 MET cc_start: 0.7261 (ttm) cc_final: 0.6925 (ttm) REVERT: D 710 GLU cc_start: 0.9504 (mt-10) cc_final: 0.9010 (tt0) outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.0676 time to fit residues: 6.2878 Evaluate side-chains 48 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 200 optimal weight: 10.0000 chunk 84 optimal weight: 0.0870 chunk 86 optimal weight: 0.9990 chunk 228 optimal weight: 9.9990 chunk 25 optimal weight: 0.0370 chunk 211 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 305 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 overall best weight: 1.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 619 ASN C1181 HIS C1229 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 791 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.070323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.055094 restraints weight = 47226.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.056642 restraints weight = 27642.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.057730 restraints weight = 19072.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.058474 restraints weight = 14609.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.058882 restraints weight = 12067.643| |-----------------------------------------------------------------------------| r_work (final): 0.3250 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.063863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050417 restraints weight = 40030.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.051632 restraints weight = 26361.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.052502 restraints weight = 19590.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.053116 restraints weight = 15850.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.053509 restraints weight = 13566.097| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.6852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28068 Z= 0.127 Angle : 0.594 11.747 37976 Z= 0.311 Chirality : 0.043 0.173 4220 Planarity : 0.004 0.051 4756 Dihedral : 5.371 61.269 3786 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.69 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.15), residues: 3452 helix: 1.16 (0.13), residues: 1634 sheet: -1.82 (0.24), residues: 432 loop : -0.94 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 628 TYR 0.027 0.001 TYR A1135 PHE 0.030 0.001 PHE C 517 TRP 0.026 0.002 TRP A 323 HIS 0.006 0.001 HIS C1181 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (28058) covalent geometry : angle 0.59424 / 0.31 (37956) SS BOND : bond 0.00112 / 0.07 ( 10) SS BOND : angle 0.59393 / 0.40 ( 20) hydrogen bonds : bond 0.03237 / 2.16 ( 1207) hydrogen bonds : angle 4.66663 / 3.34 ( 3525) ********************** REFINEMENT MACRO_CYCLE 10 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 104 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 ASP cc_start: 0.9256 (t70) cc_final: 0.8956 (p0) REVERT: C 152 SER cc_start: 0.9519 (m) cc_final: 0.9278 (p) REVERT: C 232 LEU cc_start: 0.8623 (pt) cc_final: 0.8316 (mm) REVERT: C 292 MET cc_start: 0.8812 (tmm) cc_final: 0.8574 (tmm) REVERT: C 358 ILE cc_start: 0.9374 (mt) cc_final: 0.9109 (mp) REVERT: C 380 MET cc_start: 0.8412 (mmm) cc_final: 0.8068 (mmm) REVERT: C 384 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7434 (tm-30) REVERT: C 408 MET cc_start: 0.8815 (mmm) cc_final: 0.8106 (mmm) REVERT: C 424 TYR cc_start: 0.8939 (t80) cc_final: 0.8437 (t80) REVERT: C 427 ASP cc_start: 0.9157 (m-30) cc_final: 0.8698 (m-30) REVERT: C 486 GLU cc_start: 0.8393 (tt0) cc_final: 0.8061 (tm-30) REVERT: C 503 MET cc_start: 0.9237 (ptm) cc_final: 0.8574 (ppp) REVERT: C 526 TRP cc_start: 0.8017 (m100) cc_final: 0.7071 (m100) REVERT: C 629 MET cc_start: 0.9051 (tpp) cc_final: 0.8753 (tmm) REVERT: C 644 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7671 (tp30) REVERT: C 670 MET cc_start: 0.9110 (mtm) cc_final: 0.8909 (mtm) REVERT: C 705 GLU cc_start: 0.9135 (mp0) cc_final: 0.8900 (mp0) REVERT: C 707 THR cc_start: 0.9456 (p) cc_final: 0.9115 (t) REVERT: C 708 MET cc_start: 0.9114 (tpt) cc_final: 0.8793 (tpt) REVERT: C 710 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8623 (tp30) REVERT: C 1032 TRP cc_start: 0.8265 (t-100) cc_final: 0.7040 (t60) REVERT: C 1184 TYR cc_start: 0.8720 (t80) cc_final: 0.8130 (t80) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0653 time to fit residues: 10.3087 Evaluate side-chains 88 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.283 Evaluate side-chains 63 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 54 ASN cc_start: 0.9083 (t0) cc_final: 0.8824 (p0) REVERT: D 113 MET cc_start: 0.8709 (tpt) cc_final: 0.8479 (tpp) REVERT: D 194 LEU cc_start: 0.9436 (mm) cc_final: 0.8945 (tp) REVERT: D 196 CYS cc_start: 0.7905 (m) cc_final: 0.7704 (m) REVERT: D 425 CYS cc_start: 0.9469 (m) cc_final: 0.9198 (m) REVERT: D 463 MET cc_start: 0.8711 (pmm) cc_final: 0.8470 (pmm) REVERT: D 503 MET cc_start: 0.8605 (ptm) cc_final: 0.8384 (ptp) REVERT: D 517 PHE cc_start: 0.8199 (t80) cc_final: 0.7954 (t80) REVERT: D 629 MET cc_start: 0.7272 (ttm) cc_final: 0.7048 (ttm) REVERT: D 697 LYS cc_start: 0.9104 (ptmm) cc_final: 0.8847 (ptmm) REVERT: D 710 GLU cc_start: 0.9488 (mt-10) cc_final: 0.8972 (tt0) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0611 time to fit residues: 5.7519 Evaluate side-chains 47 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 173 optimal weight: 8.9990 chunk 278 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 318 optimal weight: 6.9990 chunk 253 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 355 ASN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN C1229 ASN D 24 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.067940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.052854 restraints weight = 47684.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.054305 restraints weight = 28410.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.055331 restraints weight = 19848.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.056028 restraints weight = 15344.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.056464 restraints weight = 12774.435| |-----------------------------------------------------------------------------| r_work (final): 0.3190 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.061772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.048236 restraints weight = 41497.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.049449 restraints weight = 27052.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.050292 restraints weight = 20027.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.050929 restraints weight = 16158.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.051322 restraints weight = 13803.521| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.7106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28068 Z= 0.210 Angle : 0.661 13.035 37976 Z= 0.349 Chirality : 0.043 0.179 4220 Planarity : 0.004 0.054 4756 Dihedral : 5.581 63.674 3786 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.50 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.15), residues: 3452 helix: 0.93 (0.13), residues: 1638 sheet: -1.84 (0.25), residues: 426 loop : -0.98 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 628 TYR 0.027 0.002 TYR A1135 PHE 0.027 0.002 PHE C 517 TRP 0.024 0.002 TRP A 323 HIS 0.005 0.001 HIS C1202 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 (28058) covalent geometry : angle 0.66092 / 0.35 (37956) SS BOND : bond 0.00130 / 0.08 ( 10) SS BOND : angle 0.34720 / 0.24 ( 20) hydrogen bonds : bond 0.03615 / 2.37 ( 1207) hydrogen bonds : angle 4.99468 / 3.57 ( 3525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2871.46 seconds wall clock time: 51 minutes 32.09 seconds (3092.09 seconds total)