Starting phenix.real_space_refine on Wed Nov 19 21:21:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5wek_8819/11_2025/5wek_8819.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wek_8819/11_2025/5wek_8819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5wek_8819/11_2025/5wek_8819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wek_8819/11_2025/5wek_8819.map" model { file = "/net/cci-nas-00/data/ceres_data/5wek_8819/11_2025/5wek_8819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wek_8819/11_2025/5wek_8819.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: 6.99, per 1000 atoms: 0.25 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: 2.51 Conformation dependent library (CDL) restraints added in 1.3 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: 1.28 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: 6.21 Time building geometry restraints manager: 3.36 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: 16310 21.33 - 42.66: 284 42.66 - 64.00: 37 64.00 - 85.33: 7 85.33 - 106.66: 2 Dihedral angle restraints: 16640 sinusoidal: 6616 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 16637 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: 2.590 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: 0.100 Process input model: 28.100 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.204 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 : 9.275 106.660 10202 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 covalent geometry : bond 0.00637 (28058) covalent geometry : angle 0.93004 (37956) SS BOND : bond 0.00459 ( 10) SS BOND : angle 1.28395 ( 20) hydrogen bonds : bond 0.27449 ( 1207) hydrogen bonds : angle 10.14457 ( 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 : 0.317 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: 0.8806 (p0) outliers start: 2 outliers final: 0 residues processed: 224 average time/residue: 0.1039 time to fit residues: 30.5384 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 : 0.318 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 : 0.261 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: 0.8263 (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: 0.1097 time to fit residues: 24.2998 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 : 0.274 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 167 ASN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A1016 ASN A1037 GLN A1092 HIS A1229 ASN Total number of N/Q/H flips: 7 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN D 112 GLN D 167 ASN D 335 GLN D 359 ASN D 392 GLN D 412 HIS D 714 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.072596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.057685 restraints weight = 46385.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.059301 restraints weight = 27483.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.060340 restraints weight = 19026.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.061140 restraints weight = 14587.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.061618 restraints weight = 11989.116| |-----------------------------------------------------------------------------| r_work (final): 0.3328 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.063631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.049806 restraints weight = 40444.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.051133 restraints weight = 26028.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.052021 restraints weight = 19083.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.052728 restraints weight = 15338.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.053131 restraints weight = 12965.783| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28068 Z= 0.190 Angle : 0.679 15.080 37976 Z= 0.366 Chirality : 0.044 0.239 4220 Planarity : 0.006 0.090 4756 Dihedral : 6.779 78.629 3842 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.69 % Favored : 95.13 % Rotamer: Outliers : 0.20 % Allowed : 3.11 % Favored : 96.68 % 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: -2.40 (0.13), residues: 3452 helix: -1.23 (0.11), residues: 1638 sheet: -2.39 (0.21), residues: 440 loop : -1.53 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 628 TYR 0.021 0.002 TYR D 177 PHE 0.023 0.002 PHE D 623 TRP 0.017 0.002 TRP A 578 HIS 0.004 0.001 HIS A1202 Details of bonding type rmsd covalent geometry : bond 0.00384 (28058) covalent geometry : angle 0.67892 (37956) SS BOND : bond 0.00138 ( 10) SS BOND : angle 1.02659 ( 20) hydrogen bonds : bond 0.05206 ( 1207) hydrogen bonds : angle 6.18354 ( 3525) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 0.306 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: 0.9735 (tt) cc_final: 0.9501 (pp) REVERT: A 138 ASP cc_start: 0.8096 (t0) cc_final: 0.7718 (p0) REVERT: A 152 SER cc_start: 0.9403 (m) cc_final: 0.9141 (t) REVERT: A 193 ILE cc_start: 0.9657 (mt) cc_final: 0.9331 (mm) REVERT: A 196 CYS cc_start: 0.7997 (m) cc_final: 0.7132 (m) REVERT: A 221 ILE cc_start: 0.9536 (mt) cc_final: 0.9177 (mt) REVERT: A 384 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7523 (pp20) REVERT: A 408 MET cc_start: 0.8736 (mmm) cc_final: 0.7990 (mmm) REVERT: A 427 ASP cc_start: 0.9084 (m-30) cc_final: 0.8737 (m-30) REVERT: A 442 LEU cc_start: 0.9323 (mt) cc_final: 0.9085 (mt) REVERT: A 456 ASP cc_start: 0.8972 (m-30) cc_final: 0.8455 (p0) REVERT: A 517 PHE cc_start: 0.7612 (t80) cc_final: 0.7292 (t80) REVERT: A 527 MET cc_start: 0.6231 (mtt) cc_final: 0.5476 (mtt) REVERT: A 625 THR cc_start: 0.9677 (m) cc_final: 0.9459 (t) REVERT: A 644 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7954 (tp30) REVERT: A 670 MET cc_start: 0.9411 (mtp) cc_final: 0.9120 (mtt) REVERT: A 705 GLU cc_start: 0.9142 (mp0) cc_final: 0.8859 (mp0) REVERT: A 707 THR cc_start: 0.9323 (p) cc_final: 0.8278 (t) REVERT: A 710 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8603 (mt-10) REVERT: A 721 MET cc_start: 0.8482 (ptp) cc_final: 0.8281 (ptm) REVERT: A 1111 ARG cc_start: 0.8679 (ttm110) cc_final: 0.8293 (ptt-90) REVERT: A 1135 TYR cc_start: 0.8369 (t80) cc_final: 0.8140 (t80) REVERT: A 1184 TYR cc_start: 0.8770 (t80) cc_final: 0.8445 (t80) REVERT: A 1198 ASP cc_start: 0.9346 (m-30) cc_final: 0.8880 (p0) REVERT: A 1228 LEU cc_start: 0.9334 (mt) cc_final: 0.9093 (mt) outliers start: 2 outliers final: 1 residues processed: 148 average time/residue: 0.0992 time to fit residues: 19.6234 Evaluate side-chains 104 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.281 Evaluate side-chains 97 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: D 54 ASN cc_start: 0.8957 (t0) cc_final: 0.8578 (p0) REVERT: D 361 MET cc_start: 0.8219 (mmm) cc_final: 0.7810 (mmm) REVERT: D 408 MET cc_start: 0.7905 (mmm) cc_final: 0.7578 (mmm) REVERT: D 425 CYS cc_start: 0.9597 (m) cc_final: 0.9260 (m) REVERT: D 503 MET cc_start: 0.9038 (ptm) cc_final: 0.8536 (ptp) REVERT: D 517 PHE cc_start: 0.7861 (t80) cc_final: 0.7371 (t80) REVERT: D 704 LEU cc_start: 0.9134 (tp) cc_final: 0.8408 (tt) REVERT: D 710 GLU cc_start: 0.9462 (mt-10) cc_final: 0.8962 (tp30) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.0685 time to fit residues: 9.4261 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 : 0.253 ------------------------------------------------------------------------------- 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: 10.0000 chunk 339 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 181 optimal weight: 0.0040 chunk 221 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 overall best weight: 2.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 HIS C1016 ASN C1181 HIS C1229 ASN Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 GLN D 147 GLN D 214 HIS D 219 HIS D 359 ASN D 508 GLN D 764 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.071714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.056064 restraints weight = 45901.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.057651 restraints weight = 27701.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.058743 restraints weight = 19337.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.059500 restraints weight = 14852.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.060033 restraints weight = 12247.682| |-----------------------------------------------------------------------------| r_work (final): 0.3280 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.062915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.049286 restraints weight = 40016.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.050518 restraints weight = 26035.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.051448 restraints weight = 19264.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.052048 restraints weight = 15402.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.052567 restraints weight = 13114.427| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28068 Z= 0.143 Angle : 0.607 13.203 37976 Z= 0.324 Chirality : 0.043 0.257 4220 Planarity : 0.005 0.108 4756 Dihedral : 6.119 69.868 3842 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.68 % Favored : 94.15 % Rotamer: Outliers : 0.20 % Allowed : 3.65 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z 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: -1.67 (0.13), residues: 3452 helix: -0.34 (0.12), residues: 1628 sheet: -2.21 (0.22), residues: 432 loop : -1.52 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 660 TYR 0.018 0.001 TYR C1206 PHE 0.021 0.001 PHE A 623 TRP 0.023 0.002 TRP A1208 HIS 0.004 0.001 HIS C1202 Details of bonding type rmsd covalent geometry : bond 0.00298 (28058) covalent geometry : angle 0.60666 (37956) SS BOND : bond 0.00243 ( 10) SS BOND : angle 0.89733 ( 20) hydrogen bonds : bond 0.04023 ( 1207) hydrogen bonds : angle 5.46147 ( 3525) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 GLN cc_start: 0.8998 (mt0) cc_final: 0.8786 (pm20) REVERT: C 152 SER cc_start: 0.9395 (m) cc_final: 0.9094 (t) REVERT: C 196 CYS cc_start: 0.7963 (m) cc_final: 0.6867 (m) REVERT: C 221 ILE cc_start: 0.9633 (mt) cc_final: 0.9360 (mm) REVERT: C 232 LEU cc_start: 0.8392 (pt) cc_final: 0.8118 (mp) REVERT: C 408 MET cc_start: 0.8826 (mmm) cc_final: 0.8246 (mmm) REVERT: C 424 TYR cc_start: 0.9171 (t80) cc_final: 0.8678 (t80) REVERT: C 427 ASP cc_start: 0.9092 (m-30) cc_final: 0.8662 (m-30) REVERT: C 479 LEU cc_start: 0.9271 (tp) cc_final: 0.8861 (tp) REVERT: C 486 GLU cc_start: 0.8335 (tt0) cc_final: 0.7758 (tm-30) REVERT: C 491 PHE cc_start: 0.8692 (m-10) cc_final: 0.8404 (m-10) REVERT: C 503 MET cc_start: 0.9149 (ptm) cc_final: 0.8849 (ppp) REVERT: C 527 MET cc_start: 0.6343 (mtt) cc_final: 0.5697 (ttt) REVERT: C 644 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8090 (tp30) REVERT: C 705 GLU cc_start: 0.9167 (mp0) cc_final: 0.8805 (mp0) REVERT: C 707 THR cc_start: 0.9390 (p) cc_final: 0.8467 (t) REVERT: C 708 MET cc_start: 0.8854 (tpt) cc_final: 0.8403 (tpt) REVERT: C 722 LYS cc_start: 0.8662 (tttt) cc_final: 0.8107 (mtpt) REVERT: C 746 VAL cc_start: 0.9543 (t) cc_final: 0.9319 (p) REVERT: C 1184 TYR cc_start: 0.8662 (t80) cc_final: 0.8356 (t80) REVERT: C 1198 ASP cc_start: 0.9204 (m-30) cc_final: 0.8822 (p0) REVERT: C 1214 TRP cc_start: 0.8037 (m-10) cc_final: 0.7808 (m-10) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.0765 time to fit residues: 14.6660 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 : 0.296 Evaluate side-chains 89 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: D 54 ASN cc_start: 0.9004 (t0) cc_final: 0.8708 (p0) REVERT: D 131 ASP cc_start: 0.7826 (p0) cc_final: 0.6848 (t0) REVERT: D 284 LEU cc_start: 0.9526 (mt) cc_final: 0.9177 (mt) REVERT: D 359 ASN cc_start: 0.9364 (m-40) cc_final: 0.8620 (m-40) REVERT: D 361 MET cc_start: 0.8242 (mmm) cc_final: 0.7837 (mmm) REVERT: D 363 LEU cc_start: 0.8630 (mt) cc_final: 0.8148 (mt) REVERT: D 425 CYS cc_start: 0.9530 (m) cc_final: 0.9175 (m) REVERT: D 463 MET cc_start: 0.8992 (ptp) cc_final: 0.8698 (ptp) REVERT: D 503 MET cc_start: 0.8859 (ptm) cc_final: 0.8402 (ptp) REVERT: D 517 PHE cc_start: 0.7768 (t80) cc_final: 0.7488 (t80) REVERT: D 577 LEU cc_start: 0.8885 (tp) cc_final: 0.8672 (pp) REVERT: D 629 MET cc_start: 0.7652 (mmt) cc_final: 0.7241 (mmt) REVERT: D 633 ILE cc_start: 0.9180 (mm) cc_final: 0.8947 (mp) REVERT: D 704 LEU cc_start: 0.9142 (tp) cc_final: 0.8563 (tt) REVERT: D 710 GLU cc_start: 0.9412 (mt-10) cc_final: 0.8974 (tt0) REVERT: D 730 LYS cc_start: 0.8566 (mmpt) cc_final: 0.8352 (mmmm) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.0653 time to fit residues: 8.3218 Evaluate side-chains 65 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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: 9.9990 chunk 163 optimal weight: 9.9990 chunk 272 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 301 optimal weight: 7.9990 chunk 337 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 186 optimal weight: 0.0170 chunk 156 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 341 optimal weight: 0.1980 overall best weight: 3.4424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 355 ASN C1181 HIS C1229 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.069882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.054635 restraints weight = 47307.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.056216 restraints weight = 28554.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.057279 restraints weight = 19909.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.057986 restraints weight = 15305.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.058541 restraints weight = 12689.062| |-----------------------------------------------------------------------------| r_work (final): 0.3243 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.061757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.048032 restraints weight = 41194.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.049265 restraints weight = 26846.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.050035 restraints weight = 19923.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.050768 restraints weight = 16205.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.051224 restraints weight = 13735.372| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28068 Z= 0.168 Angle : 0.598 12.548 37976 Z= 0.320 Chirality : 0.042 0.189 4220 Planarity : 0.004 0.058 4756 Dihedral : 5.727 66.817 3842 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.97 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: -1.59 (0.13), residues: 3452 helix: -0.23 (0.12), residues: 1642 sheet: -2.35 (0.21), residues: 452 loop : -1.46 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 628 TYR 0.013 0.001 TYR C1184 PHE 0.015 0.001 PHE C 584 TRP 0.050 0.002 TRP A 578 HIS 0.004 0.001 HIS A1202 Details of bonding type rmsd covalent geometry : bond 0.00353 (28058) covalent geometry : angle 0.59768 (37956) SS BOND : bond 0.00129 ( 10) SS BOND : angle 0.72101 ( 20) hydrogen bonds : bond 0.03658 ( 1207) hydrogen bonds : angle 5.31424 ( 3525) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 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 : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 SER cc_start: 0.9437 (m) cc_final: 0.9060 (p) REVERT: C 221 ILE cc_start: 0.9652 (mt) cc_final: 0.9416 (mm) REVERT: C 232 LEU cc_start: 0.8647 (pt) cc_final: 0.8359 (mp) REVERT: C 358 ILE cc_start: 0.9341 (mt) cc_final: 0.9076 (mp) REVERT: C 408 MET cc_start: 0.8855 (mmm) cc_final: 0.8270 (mmm) REVERT: C 424 TYR cc_start: 0.9199 (t80) cc_final: 0.8677 (t80) REVERT: C 427 ASP cc_start: 0.9107 (m-30) cc_final: 0.8680 (m-30) REVERT: C 486 GLU cc_start: 0.8430 (tt0) cc_final: 0.7960 (tm-30) REVERT: C 503 MET cc_start: 0.9172 (ptm) cc_final: 0.8545 (ppp) REVERT: C 527 MET cc_start: 0.6679 (mtt) cc_final: 0.6065 (ttt) REVERT: C 644 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8015 (tp30) REVERT: C 705 GLU cc_start: 0.9198 (mp0) cc_final: 0.8866 (mp0) REVERT: C 707 THR cc_start: 0.9511 (p) cc_final: 0.8660 (t) REVERT: C 708 MET cc_start: 0.9033 (tpt) cc_final: 0.8415 (tpt) REVERT: C 1184 TYR cc_start: 0.8719 (t80) cc_final: 0.8416 (t80) REVERT: C 1198 ASP cc_start: 0.9157 (m-30) cc_final: 0.8805 (p0) REVERT: C 1199 TRP cc_start: 0.7911 (p-90) cc_final: 0.7622 (p-90) REVERT: C 1214 TRP cc_start: 0.8312 (m-10) cc_final: 0.8080 (m-10) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0798 time to fit residues: 13.1256 Evaluate side-chains 84 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.224 Evaluate side-chains 78 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 ASN cc_start: 0.9013 (t0) cc_final: 0.8756 (p0) REVERT: D 88 PHE cc_start: 0.8324 (m-10) cc_final: 0.8004 (m-10) REVERT: D 194 LEU cc_start: 0.9554 (tt) cc_final: 0.9219 (tt) REVERT: D 359 ASN cc_start: 0.9338 (m-40) cc_final: 0.8614 (m-40) REVERT: D 363 LEU cc_start: 0.8693 (mt) cc_final: 0.8302 (mt) REVERT: D 407 MET cc_start: 0.8435 (mmm) cc_final: 0.7965 (mpp) REVERT: D 425 CYS cc_start: 0.9597 (m) cc_final: 0.9209 (m) REVERT: D 463 MET cc_start: 0.8795 (ptp) cc_final: 0.8561 (ptp) REVERT: D 503 MET cc_start: 0.8847 (ptm) cc_final: 0.8391 (ptp) REVERT: D 517 PHE cc_start: 0.7988 (t80) cc_final: 0.7722 (t80) REVERT: D 704 LEU cc_start: 0.9161 (tp) cc_final: 0.8614 (tt) REVERT: D 730 LYS cc_start: 0.8696 (mmpt) cc_final: 0.8466 (mmmm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0666 time to fit residues: 7.4992 Evaluate side-chains 60 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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: 8.9990 chunk 97 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 282 optimal weight: 0.0770 chunk 263 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 chunk 280 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 322 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1181 HIS C1229 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.070100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.054826 restraints weight = 46643.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.056410 restraints weight = 27561.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.057507 restraints weight = 19037.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.058270 restraints weight = 14531.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.058824 restraints weight = 11920.268| |-----------------------------------------------------------------------------| r_work (final): 0.3252 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.061885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.048241 restraints weight = 41478.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.049473 restraints weight = 27238.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.050359 restraints weight = 20217.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.050924 restraints weight = 16292.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.051426 restraints weight = 13957.808| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28068 Z= 0.135 Angle : 0.574 12.657 37976 Z= 0.304 Chirality : 0.042 0.220 4220 Planarity : 0.004 0.058 4756 Dihedral : 5.607 64.994 3842 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.91 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -1.51 (0.14), residues: 3452 helix: -0.11 (0.12), residues: 1644 sheet: -2.33 (0.22), residues: 442 loop : -1.50 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 628 TYR 0.015 0.001 TYR A1135 PHE 0.016 0.001 PHE C 623 TRP 0.031 0.002 TRP A 578 HIS 0.004 0.001 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00282 (28058) covalent geometry : angle 0.57366 (37956) SS BOND : bond 0.00121 ( 10) SS BOND : angle 0.80649 ( 20) hydrogen bonds : bond 0.03442 ( 1207) hydrogen bonds : angle 5.06495 ( 3525) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 SER cc_start: 0.9425 (m) cc_final: 0.9058 (p) REVERT: C 232 LEU cc_start: 0.8582 (pt) cc_final: 0.8305 (mp) REVERT: C 249 ASP cc_start: 0.7156 (t0) cc_final: 0.6931 (t0) REVERT: C 358 ILE cc_start: 0.9328 (mt) cc_final: 0.9060 (mp) REVERT: C 380 MET cc_start: 0.8634 (mmm) cc_final: 0.8375 (mmm) REVERT: C 408 MET cc_start: 0.8842 (mmm) cc_final: 0.8296 (mmm) REVERT: C 424 TYR cc_start: 0.9114 (t80) cc_final: 0.8672 (t80) REVERT: C 427 ASP cc_start: 0.9129 (m-30) cc_final: 0.8696 (m-30) REVERT: C 486 GLU cc_start: 0.8406 (tt0) cc_final: 0.7937 (tm-30) REVERT: C 503 MET cc_start: 0.9170 (ptm) cc_final: 0.8596 (ppp) REVERT: C 527 MET cc_start: 0.6740 (mtt) cc_final: 0.6258 (ttt) REVERT: C 644 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7926 (tp30) REVERT: C 705 GLU cc_start: 0.9146 (mp0) cc_final: 0.8823 (mp0) REVERT: C 707 THR cc_start: 0.9508 (p) cc_final: 0.8677 (t) REVERT: C 708 MET cc_start: 0.9044 (tpt) cc_final: 0.8677 (tpt) REVERT: C 1169 PHE cc_start: 0.8756 (m-80) cc_final: 0.8428 (m-80) REVERT: C 1184 TYR cc_start: 0.8680 (t80) cc_final: 0.8428 (t80) REVERT: C 1199 TRP cc_start: 0.7909 (p-90) cc_final: 0.7627 (p-90) REVERT: C 1214 TRP cc_start: 0.8488 (m-10) cc_final: 0.8118 (m-10) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0755 time to fit residues: 11.9903 Evaluate side-chains 83 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.284 Evaluate side-chains 77 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 ASN cc_start: 0.9070 (t0) cc_final: 0.8808 (p0) REVERT: D 88 PHE cc_start: 0.8352 (m-10) cc_final: 0.7998 (m-10) REVERT: D 358 ILE cc_start: 0.9394 (mt) cc_final: 0.9157 (mt) REVERT: D 359 ASN cc_start: 0.9230 (m-40) cc_final: 0.8962 (t0) REVERT: D 363 LEU cc_start: 0.8704 (mt) cc_final: 0.8214 (mt) REVERT: D 407 MET cc_start: 0.8407 (mmm) cc_final: 0.7925 (mpp) REVERT: D 425 CYS cc_start: 0.9560 (m) cc_final: 0.9130 (m) REVERT: D 491 PHE cc_start: 0.7217 (m-80) cc_final: 0.6833 (m-80) REVERT: D 503 MET cc_start: 0.8790 (ptm) cc_final: 0.8356 (ptp) REVERT: D 517 PHE cc_start: 0.8143 (t80) cc_final: 0.7888 (t80) REVERT: D 710 GLU cc_start: 0.9409 (mt-10) cc_final: 0.8947 (tt0) REVERT: D 730 LYS cc_start: 0.8687 (mmpt) cc_final: 0.8476 (mmmm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0781 time to fit residues: 8.2652 Evaluate side-chains 57 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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: 2.9990 chunk 72 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 327 optimal weight: 0.0070 chunk 163 optimal weight: 4.9990 chunk 94 optimal weight: 0.3980 chunk 168 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1181 HIS C1229 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 GLN D 311 ASN ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.071466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.056201 restraints weight = 45588.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.057820 restraints weight = 27055.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.058939 restraints weight = 18657.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.059709 restraints weight = 14174.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.060261 restraints weight = 11597.877| |-----------------------------------------------------------------------------| r_work (final): 0.3290 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.063450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.049648 restraints weight = 40226.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.050870 restraints weight = 26322.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.051776 restraints weight = 19607.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.052439 restraints weight = 15708.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.052858 restraints weight = 13340.985| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.6091 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= 0.108 Angle : 0.563 11.834 37976 Z= 0.296 Chirality : 0.042 0.225 4220 Planarity : 0.004 0.052 4756 Dihedral : 5.359 61.948 3842 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.39 % Favored : 94.38 % Rotamer: Outliers : 0.07 % Allowed : 2.17 % Favored : 97.77 % 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: -1.37 (0.14), residues: 3452 helix: 0.06 (0.12), residues: 1642 sheet: -2.23 (0.22), residues: 450 loop : -1.52 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 660 TYR 0.015 0.001 TYR A1135 PHE 0.014 0.001 PHE A 623 TRP 0.025 0.002 TRP C 578 HIS 0.003 0.000 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00230 (28058) covalent geometry : angle 0.56310 (37956) SS BOND : bond 0.00086 ( 10) SS BOND : angle 0.67668 ( 20) hydrogen bonds : bond 0.03100 ( 1207) hydrogen bonds : angle 4.82955 ( 3525) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 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 : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 SER cc_start: 0.9377 (m) cc_final: 0.9144 (p) REVERT: C 232 LEU cc_start: 0.8478 (pt) cc_final: 0.8173 (mp) REVERT: C 249 ASP cc_start: 0.7232 (t0) cc_final: 0.7004 (t0) REVERT: C 358 ILE cc_start: 0.9300 (mt) cc_final: 0.9084 (mp) REVERT: C 380 MET cc_start: 0.8636 (mmm) cc_final: 0.8373 (mmm) REVERT: C 384 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7440 (tm-30) REVERT: C 408 MET cc_start: 0.8799 (mmm) cc_final: 0.8263 (mmm) REVERT: C 424 TYR cc_start: 0.9008 (t80) cc_final: 0.8519 (t80) REVERT: C 427 ASP cc_start: 0.9110 (m-30) cc_final: 0.8664 (m-30) REVERT: C 474 ILE cc_start: 0.9072 (tt) cc_final: 0.8613 (mm) REVERT: C 486 GLU cc_start: 0.8278 (tt0) cc_final: 0.7845 (tm-30) REVERT: C 503 MET cc_start: 0.9081 (ptm) cc_final: 0.8555 (ppp) REVERT: C 526 TRP cc_start: 0.7557 (m100) cc_final: 0.6429 (m100) REVERT: C 527 MET cc_start: 0.6472 (mtt) cc_final: 0.6081 (ttt) REVERT: C 705 GLU cc_start: 0.9017 (mp0) cc_final: 0.8738 (mp0) REVERT: C 707 THR cc_start: 0.9444 (p) cc_final: 0.8982 (t) REVERT: C 722 LYS cc_start: 0.8671 (tttt) cc_final: 0.8127 (tttm) REVERT: C 1021 LEU cc_start: 0.7892 (mt) cc_final: 0.7665 (tp) REVERT: C 1169 PHE cc_start: 0.8763 (m-80) cc_final: 0.8424 (m-80) REVERT: C 1184 TYR cc_start: 0.8584 (t80) cc_final: 0.8346 (t80) REVERT: C 1214 TRP cc_start: 0.8397 (m-10) cc_final: 0.7754 (m-10) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0761 time to fit residues: 12.7373 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 : 0.297 Evaluate side-chains 82 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 54 ASN cc_start: 0.9080 (t0) cc_final: 0.8780 (p0) REVERT: D 88 PHE cc_start: 0.8368 (m-10) cc_final: 0.8023 (m-10) REVERT: D 358 ILE cc_start: 0.9377 (mt) cc_final: 0.9111 (mm) REVERT: D 359 ASN cc_start: 0.9213 (m-40) cc_final: 0.8586 (m-40) REVERT: D 425 CYS cc_start: 0.9550 (m) cc_final: 0.9109 (m) REVERT: D 463 MET cc_start: 0.8916 (ptp) cc_final: 0.8347 (ppp) REVERT: D 491 PHE cc_start: 0.7195 (m-80) cc_final: 0.6834 (m-80) REVERT: D 503 MET cc_start: 0.8767 (ptm) cc_final: 0.8390 (ptp) REVERT: D 517 PHE cc_start: 0.8047 (t80) cc_final: 0.7758 (t80) REVERT: D 668 ASP cc_start: 0.9350 (t0) cc_final: 0.9114 (m-30) REVERT: D 708 MET cc_start: 0.8915 (tpp) cc_final: 0.8272 (ttm) REVERT: D 710 GLU cc_start: 0.9435 (mt-10) cc_final: 0.9013 (tt0) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.0796 time to fit residues: 8.8275 Evaluate side-chains 51 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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: 3.9990 chunk 283 optimal weight: 0.0970 chunk 90 optimal weight: 20.0000 chunk 186 optimal weight: 0.3980 chunk 91 optimal weight: 9.9990 chunk 71 optimal weight: 0.0040 chunk 166 optimal weight: 2.9990 chunk 271 optimal weight: 8.9990 chunk 335 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 263 optimal weight: 0.0970 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1181 HIS C1229 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 GLN D 147 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: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.072202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.057259 restraints weight = 45280.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058845 restraints weight = 27576.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.059930 restraints weight = 19232.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.060599 restraints weight = 14734.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.061185 restraints weight = 12259.582| |-----------------------------------------------------------------------------| r_work (final): 0.3307 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.064506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.050972 restraints weight = 40377.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.052275 restraints weight = 26365.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.053195 restraints weight = 19304.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.053803 restraints weight = 15421.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.054280 restraints weight = 13153.006| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.6345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 28068 Z= 0.107 Angle : 0.572 13.072 37976 Z= 0.296 Chirality : 0.042 0.202 4220 Planarity : 0.004 0.111 4756 Dihedral : 5.335 61.688 3842 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.45 % Favored : 94.32 % Rotamer: Outliers : 0.07 % Allowed : 0.88 % Favored : 99.05 % 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: -1.29 (0.14), residues: 3452 helix: 0.15 (0.12), residues: 1618 sheet: -2.19 (0.22), residues: 452 loop : -1.49 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A 628 TYR 0.016 0.001 TYR A1135 PHE 0.027 0.001 PHE C 517 TRP 0.043 0.002 TRP C 323 HIS 0.006 0.001 HIS C1181 Details of bonding type rmsd covalent geometry : bond 0.00228 (28058) covalent geometry : angle 0.57165 (37956) SS BOND : bond 0.00131 ( 10) SS BOND : angle 0.83742 ( 20) hydrogen bonds : bond 0.03094 ( 1207) hydrogen bonds : angle 4.68244 ( 3525) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 SER cc_start: 0.9500 (m) cc_final: 0.9231 (p) REVERT: C 232 LEU cc_start: 0.8596 (pt) cc_final: 0.8276 (mm) REVERT: C 249 ASP cc_start: 0.7200 (t0) cc_final: 0.6982 (t0) REVERT: C 358 ILE cc_start: 0.9385 (mt) cc_final: 0.9137 (mp) REVERT: C 384 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7449 (tm-30) REVERT: C 408 MET cc_start: 0.8794 (mmm) cc_final: 0.8220 (mmm) REVERT: C 424 TYR cc_start: 0.9076 (t80) cc_final: 0.8589 (t80) REVERT: C 425 CYS cc_start: 0.9221 (m) cc_final: 0.8983 (m) REVERT: C 427 ASP cc_start: 0.9090 (m-30) cc_final: 0.8618 (m-30) REVERT: C 474 ILE cc_start: 0.9038 (tt) cc_final: 0.8675 (mm) REVERT: C 486 GLU cc_start: 0.8491 (tt0) cc_final: 0.8013 (tm-30) REVERT: C 503 MET cc_start: 0.9168 (ptm) cc_final: 0.8609 (ppp) REVERT: C 526 TRP cc_start: 0.7624 (m100) cc_final: 0.6490 (m100) REVERT: C 527 MET cc_start: 0.6663 (mtt) cc_final: 0.6262 (ttt) REVERT: C 579 PHE cc_start: 0.7368 (m-80) cc_final: 0.7031 (m-10) REVERT: C 705 GLU cc_start: 0.9098 (mp0) cc_final: 0.8856 (mp0) REVERT: C 707 THR cc_start: 0.9411 (p) cc_final: 0.9050 (t) REVERT: C 710 GLU cc_start: 0.9373 (mm-30) cc_final: 0.8582 (tp30) REVERT: C 1025 THR cc_start: 0.8256 (m) cc_final: 0.7924 (p) REVERT: C 1169 PHE cc_start: 0.8814 (m-80) cc_final: 0.8464 (m-80) REVERT: C 1184 TYR cc_start: 0.8592 (t80) cc_final: 0.8018 (t80) REVERT: C 1214 TRP cc_start: 0.7384 (m-10) cc_final: 0.5972 (m-10) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.0670 time to fit residues: 11.0850 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 : 0.303 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 : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 54 ASN cc_start: 0.9085 (t0) cc_final: 0.8798 (p0) REVERT: D 358 ILE cc_start: 0.9363 (mt) cc_final: 0.9083 (mm) REVERT: D 359 ASN cc_start: 0.9110 (m-40) cc_final: 0.8494 (m-40) REVERT: D 425 CYS cc_start: 0.9505 (m) cc_final: 0.9160 (m) REVERT: D 463 MET cc_start: 0.8957 (ptp) cc_final: 0.8377 (ppp) REVERT: D 491 PHE cc_start: 0.7232 (m-80) cc_final: 0.6871 (m-80) REVERT: D 503 MET cc_start: 0.8684 (ptm) cc_final: 0.8392 (ptp) REVERT: D 668 ASP cc_start: 0.9277 (t0) cc_final: 0.9018 (m-30) REVERT: D 710 GLU cc_start: 0.9496 (mt-10) cc_final: 0.9095 (tt0) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.0647 time to fit residues: 6.9984 Evaluate side-chains 51 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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: 0.9990 chunk 114 optimal weight: 5.9990 chunk 140 optimal weight: 0.0170 chunk 113 optimal weight: 4.9990 chunk 263 optimal weight: 0.4980 chunk 235 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 142 optimal weight: 0.0570 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1181 HIS C1229 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** 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: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.072105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.057172 restraints weight = 44996.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.058669 restraints weight = 27732.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.059720 restraints weight = 19607.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.060454 restraints weight = 15136.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.060971 restraints weight = 12515.418| |-----------------------------------------------------------------------------| r_work (final): 0.3301 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.064829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.051291 restraints weight = 40195.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.052546 restraints weight = 26477.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.053394 restraints weight = 19659.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.054112 restraints weight = 15811.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.054564 restraints weight = 13380.639| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.6511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 28068 Z= 0.105 Angle : 0.558 12.593 37976 Z= 0.290 Chirality : 0.041 0.185 4220 Planarity : 0.004 0.065 4756 Dihedral : 5.275 64.581 3842 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.39 % Favored : 94.38 % Rotamer: Outliers : 0.07 % Allowed : 0.88 % Favored : 99.05 % 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: -1.20 (0.14), residues: 3452 helix: 0.27 (0.12), residues: 1628 sheet: -2.26 (0.22), residues: 454 loop : -1.48 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 628 TYR 0.025 0.001 TYR D 616 PHE 0.025 0.001 PHE C1210 TRP 0.035 0.002 TRP B 323 HIS 0.005 0.001 HIS C1181 Details of bonding type rmsd covalent geometry : bond 0.00233 (28058) covalent geometry : angle 0.55747 (37956) SS BOND : bond 0.00226 ( 10) SS BOND : angle 1.28129 ( 20) hydrogen bonds : bond 0.02969 ( 1207) hydrogen bonds : angle 4.62492 ( 3525) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 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 : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 SER cc_start: 0.9503 (m) cc_final: 0.9248 (p) REVERT: C 232 LEU cc_start: 0.8599 (pt) cc_final: 0.8296 (mm) REVERT: C 249 ASP cc_start: 0.7135 (t0) cc_final: 0.6911 (t0) REVERT: C 292 MET cc_start: 0.8784 (tmm) cc_final: 0.8555 (tmm) REVERT: C 358 ILE cc_start: 0.9397 (mt) cc_final: 0.9137 (mp) REVERT: C 380 MET cc_start: 0.8519 (mmm) cc_final: 0.8146 (mmm) REVERT: C 384 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7454 (tm-30) REVERT: C 408 MET cc_start: 0.8810 (mmm) cc_final: 0.8236 (mmm) REVERT: C 424 TYR cc_start: 0.9133 (t80) cc_final: 0.8643 (t80) REVERT: C 425 CYS cc_start: 0.9253 (m) cc_final: 0.9048 (m) REVERT: C 427 ASP cc_start: 0.9107 (m-30) cc_final: 0.8617 (m-30) REVERT: C 486 GLU cc_start: 0.8614 (tt0) cc_final: 0.8198 (tm-30) REVERT: C 503 MET cc_start: 0.9202 (ptm) cc_final: 0.8652 (ppp) REVERT: C 526 TRP cc_start: 0.7678 (m100) cc_final: 0.6954 (m100) REVERT: C 527 MET cc_start: 0.6666 (mtt) cc_final: 0.6300 (ttt) REVERT: C 579 PHE cc_start: 0.7465 (m-80) cc_final: 0.6763 (m-10) REVERT: C 705 GLU cc_start: 0.9124 (mp0) cc_final: 0.8880 (mp0) REVERT: C 707 THR cc_start: 0.9386 (p) cc_final: 0.9016 (t) REVERT: C 710 GLU cc_start: 0.9403 (mm-30) cc_final: 0.9098 (tp30) REVERT: C 722 LYS cc_start: 0.8357 (tttt) cc_final: 0.7954 (mtpt) REVERT: C 1032 TRP cc_start: 0.8160 (t-100) cc_final: 0.7296 (t60) REVERT: C 1169 PHE cc_start: 0.8796 (m-80) cc_final: 0.8491 (m-80) REVERT: C 1184 TYR cc_start: 0.8508 (t80) cc_final: 0.7969 (t80) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0722 time to fit residues: 11.4810 Evaluate side-chains 85 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.325 Evaluate side-chains 68 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 54 ASN cc_start: 0.9065 (t0) cc_final: 0.8809 (p0) REVERT: D 358 ILE cc_start: 0.9383 (mt) cc_final: 0.9111 (mm) REVERT: D 359 ASN cc_start: 0.9177 (m-40) cc_final: 0.8494 (m-40) REVERT: D 425 CYS cc_start: 0.9512 (m) cc_final: 0.9239 (m) REVERT: D 463 MET cc_start: 0.8931 (ptp) cc_final: 0.8344 (ppp) REVERT: D 491 PHE cc_start: 0.7267 (m-80) cc_final: 0.6845 (m-80) REVERT: D 503 MET cc_start: 0.8745 (ptm) cc_final: 0.8469 (ptp) REVERT: D 668 ASP cc_start: 0.9300 (t0) cc_final: 0.9050 (m-30) REVERT: D 710 GLU cc_start: 0.9375 (mt-10) cc_final: 0.8937 (tt0) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.0647 time to fit residues: 6.4668 Evaluate side-chains 50 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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: 0.0050 chunk 185 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 307 optimal weight: 0.9990 chunk 151 optimal weight: 30.0000 chunk 104 optimal weight: 6.9990 chunk 326 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 303 optimal weight: 9.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1189 GLN C1229 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.069740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.054854 restraints weight = 47377.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.056410 restraints weight = 28540.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.057470 restraints weight = 19900.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.058220 restraints weight = 15350.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.058692 restraints weight = 12644.198| |-----------------------------------------------------------------------------| r_work (final): 0.3242 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.062944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049515 restraints weight = 40472.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.050701 restraints weight = 27091.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.051527 restraints weight = 20250.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.052168 restraints weight = 16402.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.052530 restraints weight = 13990.715| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 28068 Z= 0.158 Angle : 0.605 11.678 37976 Z= 0.321 Chirality : 0.042 0.275 4220 Planarity : 0.004 0.054 4756 Dihedral : 5.384 64.799 3842 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.08 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -1.25 (0.14), residues: 3452 helix: 0.22 (0.12), residues: 1666 sheet: -2.40 (0.23), residues: 424 loop : -1.52 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 628 TYR 0.030 0.001 TYR C1184 PHE 0.034 0.002 PHE C1210 TRP 0.037 0.002 TRP A1204 HIS 0.004 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00342 (28058) covalent geometry : angle 0.60522 (37956) SS BOND : bond 0.00106 ( 10) SS BOND : angle 0.67815 ( 20) hydrogen bonds : bond 0.03196 ( 1207) hydrogen bonds : angle 4.86666 ( 3525) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 SER cc_start: 0.9542 (m) cc_final: 0.9296 (p) REVERT: C 292 MET cc_start: 0.8785 (tmm) cc_final: 0.8538 (tmm) REVERT: C 358 ILE cc_start: 0.9393 (mt) cc_final: 0.9144 (mp) REVERT: C 380 MET cc_start: 0.8568 (mmm) cc_final: 0.8362 (mmm) REVERT: C 384 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7454 (tm-30) REVERT: C 408 MET cc_start: 0.8883 (mmm) cc_final: 0.8313 (mmm) REVERT: C 424 TYR cc_start: 0.9087 (t80) cc_final: 0.8647 (t80) REVERT: C 425 CYS cc_start: 0.9268 (m) cc_final: 0.9033 (m) REVERT: C 427 ASP cc_start: 0.9117 (m-30) cc_final: 0.8650 (m-30) REVERT: C 486 GLU cc_start: 0.8584 (tt0) cc_final: 0.8157 (tm-30) REVERT: C 503 MET cc_start: 0.9096 (ptm) cc_final: 0.8684 (ppp) REVERT: C 527 MET cc_start: 0.6524 (mtt) cc_final: 0.6203 (ttt) REVERT: C 579 PHE cc_start: 0.7517 (m-80) cc_final: 0.6773 (m-10) REVERT: C 629 MET cc_start: 0.9126 (tpp) cc_final: 0.8792 (tmm) REVERT: C 705 GLU cc_start: 0.9088 (mp0) cc_final: 0.8801 (mp0) REVERT: C 707 THR cc_start: 0.9458 (p) cc_final: 0.9089 (t) REVERT: C 710 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9063 (tp30) REVERT: C 722 LYS cc_start: 0.8423 (tttt) cc_final: 0.7821 (mtpt) REVERT: C 1169 PHE cc_start: 0.8751 (m-80) cc_final: 0.8454 (m-80) REVERT: C 1182 MET cc_start: 0.9244 (mpp) cc_final: 0.9021 (mpp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0809 time to fit residues: 12.0219 Evaluate side-chains 79 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.426 Evaluate side-chains 66 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 54 ASN cc_start: 0.9055 (t0) cc_final: 0.8843 (p0) REVERT: D 425 CYS cc_start: 0.9480 (m) cc_final: 0.9050 (m) REVERT: D 491 PHE cc_start: 0.7273 (m-80) cc_final: 0.7067 (m-10) REVERT: D 503 MET cc_start: 0.8684 (ptm) cc_final: 0.8444 (ptp) REVERT: D 585 MET cc_start: 0.4661 (pmm) cc_final: 0.4458 (ppp) REVERT: D 628 ARG cc_start: 0.8147 (ppt170) cc_final: 0.7607 (ttp80) REVERT: D 668 ASP cc_start: 0.9338 (t0) cc_final: 0.9092 (m-30) REVERT: D 710 GLU cc_start: 0.9464 (mt-10) cc_final: 0.9016 (tt0) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0697 time to fit residues: 6.7294 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 : 0.292 ------------------------------------------------------------------------------- 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: 0.0980 chunk 86 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 211 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 305 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 172 optimal weight: 10.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1229 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN D 587 GLN ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.068321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053741 restraints weight = 47948.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.055204 restraints weight = 28921.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.056248 restraints weight = 20329.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.056956 restraints weight = 15669.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.057448 restraints weight = 12992.853| |-----------------------------------------------------------------------------| r_work (final): 0.3210 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.061829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.048401 restraints weight = 40132.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049545 restraints weight = 26297.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.050416 restraints weight = 19649.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.050966 restraints weight = 15851.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.051423 restraints weight = 13630.311| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.7012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28068 Z= 0.167 Angle : 0.628 11.487 37976 Z= 0.333 Chirality : 0.043 0.188 4220 Planarity : 0.004 0.060 4756 Dihedral : 5.407 63.559 3842 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.26 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.33 (0.14), residues: 3452 helix: 0.11 (0.12), residues: 1658 sheet: -2.28 (0.24), residues: 404 loop : -1.57 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 628 TYR 0.018 0.001 TYR A1135 PHE 0.032 0.002 PHE A1210 TRP 0.048 0.003 TRP A1214 HIS 0.004 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00359 (28058) covalent geometry : angle 0.62816 (37956) SS BOND : bond 0.00148 ( 10) SS BOND : angle 0.62163 ( 20) hydrogen bonds : bond 0.03436 ( 1207) hydrogen bonds : angle 4.96664 ( 3525) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 SER cc_start: 0.9545 (m) cc_final: 0.9328 (p) REVERT: C 249 ASP cc_start: 0.7024 (t0) cc_final: 0.6803 (t0) REVERT: C 292 MET cc_start: 0.8752 (tmm) cc_final: 0.8528 (tmm) REVERT: C 358 ILE cc_start: 0.9381 (mt) cc_final: 0.9168 (mp) REVERT: C 408 MET cc_start: 0.8822 (mmm) cc_final: 0.8183 (mmm) REVERT: C 424 TYR cc_start: 0.9039 (t80) cc_final: 0.8580 (t80) REVERT: C 427 ASP cc_start: 0.9105 (m-30) cc_final: 0.8641 (m-30) REVERT: C 486 GLU cc_start: 0.8413 (tt0) cc_final: 0.8035 (tm-30) REVERT: C 503 MET cc_start: 0.9101 (ptm) cc_final: 0.8725 (ppp) REVERT: C 527 MET cc_start: 0.6710 (mtt) cc_final: 0.6488 (ttt) REVERT: C 579 PHE cc_start: 0.7574 (m-80) cc_final: 0.6722 (m-10) REVERT: C 623 PHE cc_start: 0.8603 (m-10) cc_final: 0.8368 (m-10) REVERT: C 624 LEU cc_start: 0.9501 (pp) cc_final: 0.9269 (pp) REVERT: C 629 MET cc_start: 0.9183 (tpp) cc_final: 0.8813 (tmm) REVERT: C 670 MET cc_start: 0.9091 (mtm) cc_final: 0.8822 (mtm) REVERT: C 705 GLU cc_start: 0.9074 (mp0) cc_final: 0.8862 (mp0) REVERT: C 707 THR cc_start: 0.9469 (p) cc_final: 0.9128 (t) REVERT: C 710 GLU cc_start: 0.9378 (mm-30) cc_final: 0.8988 (mm-30) REVERT: C 722 LYS cc_start: 0.8510 (tttt) cc_final: 0.7761 (tttt) REVERT: C 1032 TRP cc_start: 0.8792 (t-100) cc_final: 0.7884 (t60) REVERT: C 1169 PHE cc_start: 0.8794 (m-80) cc_final: 0.8492 (m-80) REVERT: C 1184 TYR cc_start: 0.8346 (t80) cc_final: 0.7945 (t80) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.0706 time to fit residues: 10.5115 Evaluate side-chains 76 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.362 Evaluate side-chains 64 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 425 CYS cc_start: 0.9420 (m) cc_final: 0.8988 (m) REVERT: D 517 PHE cc_start: 0.8212 (t80) cc_final: 0.7754 (t80) REVERT: D 628 ARG cc_start: 0.8313 (ppt170) cc_final: 0.7774 (ttp80) REVERT: D 629 MET cc_start: 0.7220 (ttm) cc_final: 0.6965 (ttm) REVERT: D 697 LYS cc_start: 0.9182 (ptmm) cc_final: 0.8901 (ptmm) REVERT: D 710 GLU cc_start: 0.9464 (mt-10) cc_final: 0.8960 (tt0) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0694 time to fit residues: 6.3700 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 : 0.297 ------------------------------------------------------------------------------- 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: 4.9990 chunk 278 optimal weight: 0.9980 chunk 151 optimal weight: 0.0370 chunk 84 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 318 optimal weight: 6.9990 chunk 253 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 GLN C1229 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.068710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.054055 restraints weight = 46979.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.055562 restraints weight = 28293.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.056594 restraints weight = 19723.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.057299 restraints weight = 15182.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.057678 restraints weight = 12582.410| |-----------------------------------------------------------------------------| r_work (final): 0.3221 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.062711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.049335 restraints weight = 40028.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.050540 restraints weight = 26276.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.051433 restraints weight = 19568.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.051991 restraints weight = 15720.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.052478 restraints weight = 13499.969| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.7115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28068 Z= 0.134 Angle : 0.614 11.525 37976 Z= 0.321 Chirality : 0.042 0.162 4220 Planarity : 0.004 0.060 4756 Dihedral : 5.401 62.400 3842 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.49 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.23 (0.14), residues: 3452 helix: 0.18 (0.13), residues: 1646 sheet: -2.25 (0.25), residues: 390 loop : -1.49 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 675 TYR 0.023 0.001 TYR B 616 PHE 0.031 0.001 PHE B 607 TRP 0.056 0.002 TRP A1214 HIS 0.005 0.001 HIS C1181 Details of bonding type rmsd covalent geometry : bond 0.00294 (28058) covalent geometry : angle 0.61412 (37956) SS BOND : bond 0.00125 ( 10) SS BOND : angle 0.63226 ( 20) hydrogen bonds : bond 0.03219 ( 1207) hydrogen bonds : angle 4.90222 ( 3525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2818.91 seconds wall clock time: 50 minutes 42.97 seconds (3042.97 seconds total)