Starting phenix.real_space_refine on Sun Jul 5 11:50:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7txv_26161/07_2026/7txv_26161.cif Found real_map, /net/cci-nas-00/data/ceres_data/7txv_26161/07_2026/7txv_26161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7txv_26161/07_2026/7txv_26161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7txv_26161/07_2026/7txv_26161.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7txv_26161/07_2026/7txv_26161.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7txv_26161/07_2026/7txv_26161.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7txv_26161/07_2026/7txv_26161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7txv_26161/07_2026/7txv_26161.map" } resolution = 2.7 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= 0.005 sd= 0.103 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 24 5.49 5 Mg 16 5.21 5 S 96 5.16 5 C 17232 2.51 5 N 4904 2.21 5 O 5372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27648 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 870, 6650 Classifications: {'peptide': 870} Link IDs: {'PTRANS': 40, 'TRANS': 829} Chain breaks: 1 Chain: "B" Number of atoms: 6650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 870, 6650 Classifications: {'peptide': 870} Link IDs: {'PTRANS': 40, 'TRANS': 829} Chain breaks: 1 Chain: "C" Number of atoms: 6650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 870, 6650 Classifications: {'peptide': 870} Link IDs: {'PTRANS': 40, 'TRANS': 829} Chain breaks: 1 Chain: "D" Number of atoms: 6650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 870, 6650 Classifications: {'peptide': 870} Link IDs: {'PTRANS': 40, 'TRANS': 829} Chain breaks: 1 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'7ID:plan-1': 1, '7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'7ID:plan-1': 1, '7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'7ID:plan-1': 1, '7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'7ID:plan-1': 1, '7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 134 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'7ID:plan-4': 8, '7ID:plan-1': 1, '7ID:plan-2': 1, '7ID:plan-3': 1} Unresolved non-hydrogen planarities: 25 Chain: "J" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 134 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'7ID:plan-4': 8, '7ID:plan-1': 1, '7ID:plan-2': 1, '7ID:plan-3': 1} Unresolved non-hydrogen planarities: 25 Chain: "K" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 134 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'7ID:plan-4': 8, '7ID:plan-1': 1, '7ID:plan-2': 1, '7ID:plan-3': 1} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 134 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'7ID:plan-4': 8, '7ID:plan-1': 1, '7ID:plan-2': 1, '7ID:plan-3': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {' MG': 4, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {' MG': 4, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {' MG': 4, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {' MG': 4, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 484 SG CYS A 59 79.190 128.854 41.252 1.00 81.08 S ATOM 7134 SG CYS B 59 69.745 19.817 41.079 1.00 87.56 S ATOM 13784 SG CYS C 59 69.725 128.953 92.285 1.00 84.85 S ATOM 20434 SG CYS D 59 79.040 19.819 92.296 1.00 85.48 S Time building chain proxies: 5.99, per 1000 atoms: 0.22 Number of scatterers: 27648 At special positions: 0 Unit cell: (149.625, 149.625, 134.235, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 96 16.00 P 24 15.00 Mg 16 11.99 O 5372 8.00 N 4904 7.00 C 17232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.43 Conformation dependent library (CDL) restraints added in 892.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 905 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A 905 " - pdb=" SG CYS A 59 " pdb=" ZN B 905 " pdb="ZN ZN B 905 " - pdb=" NE2 HIS B 83 " pdb="ZN ZN B 905 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B 905 " - pdb=" SG CYS B 59 " pdb=" ZN C 905 " pdb="ZN ZN C 905 " - pdb=" NE2 HIS C 83 " pdb="ZN ZN C 905 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C 905 " - pdb=" SG CYS C 59 " pdb=" ZN D 905 " pdb="ZN ZN D 905 " - pdb=" NE2 HIS D 83 " pdb="ZN ZN D 905 " - pdb=" NE2 HIS D 79 " pdb="ZN ZN D 905 " - pdb=" SG CYS D 59 " 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 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: 136 helices and 28 sheets defined 39.3% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.829A pdb=" N ILE A 80 " --> pdb=" O TYR A 76 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS A 83 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.343A pdb=" N ASP A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 245 through 254 removed outlier: 4.308A pdb=" N ASN A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 405 through 408 removed outlier: 4.067A pdb=" N ILE A 408 " --> pdb=" O THR A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 409 through 424 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 472 through 480 removed outlier: 3.694A pdb=" N MET A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 512 removed outlier: 3.523A pdb=" N GLN A 512 " --> pdb=" O HIS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 548 removed outlier: 3.864A pdb=" N VAL A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 594 through 607 removed outlier: 3.596A pdb=" N LYS A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.762A pdb=" N ALA A 626 " --> pdb=" O PRO A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 630 Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 690 through 707 Processing helix chain 'A' and resid 710 through 721 Processing helix chain 'A' and resid 749 through 762 removed outlier: 3.553A pdb=" N TYR A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 756 " --> pdb=" O GLY A 752 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 791 Processing helix chain 'A' and resid 810 through 824 Processing helix chain 'A' and resid 858 through 866 removed outlier: 3.618A pdb=" N ASP A 864 " --> pdb=" O THR A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 870 Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 76 through 91 removed outlier: 3.829A pdb=" N ILE B 80 " --> pdb=" O TYR B 76 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS B 83 " --> pdb=" O HIS B 79 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 86 " --> pdb=" O GLN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 136 Processing helix chain 'B' and resid 144 through 161 removed outlier: 4.342A pdb=" N ASP B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 219 through 229 Processing helix chain 'B' and resid 245 through 254 removed outlier: 4.309A pdb=" N ASN B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 289 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.066A pdb=" N ILE B 408 " --> pdb=" O THR B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 409 through 424 Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 472 through 480 removed outlier: 3.693A pdb=" N MET B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 512 removed outlier: 3.523A pdb=" N GLN B 512 " --> pdb=" O HIS B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 548 removed outlier: 3.864A pdb=" N VAL B 545 " --> pdb=" O GLN B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 594 through 607 removed outlier: 3.596A pdb=" N LYS B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 removed outlier: 3.761A pdb=" N ALA B 626 " --> pdb=" O PRO B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 630 Processing helix chain 'B' and resid 644 through 652 Processing helix chain 'B' and resid 680 through 682 No H-bonds generated for 'chain 'B' and resid 680 through 682' Processing helix chain 'B' and resid 690 through 707 Processing helix chain 'B' and resid 710 through 721 Processing helix chain 'B' and resid 749 through 762 removed outlier: 3.552A pdb=" N TYR B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL B 756 " --> pdb=" O GLY B 752 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 791 Processing helix chain 'B' and resid 810 through 824 Processing helix chain 'B' and resid 858 through 866 removed outlier: 3.618A pdb=" N ASP B 864 " --> pdb=" O THR B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 870 Processing helix chain 'C' and resid 44 through 51 Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 76 through 91 removed outlier: 3.829A pdb=" N ILE C 80 " --> pdb=" O TYR C 76 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 86 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 136 Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.342A pdb=" N ASP C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 210 through 217 Processing helix chain 'C' and resid 219 through 229 Processing helix chain 'C' and resid 245 through 254 removed outlier: 4.308A pdb=" N ASN C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 289 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 363 through 372 Processing helix chain 'C' and resid 394 through 398 Processing helix chain 'C' and resid 405 through 408 removed outlier: 4.067A pdb=" N ILE C 408 " --> pdb=" O THR C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 409 through 424 Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 457 through 462 Processing helix chain 'C' and resid 472 through 480 removed outlier: 3.693A pdb=" N MET C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 512 removed outlier: 3.523A pdb=" N GLN C 512 " --> pdb=" O HIS C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 548 removed outlier: 3.863A pdb=" N VAL C 545 " --> pdb=" O GLN C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 568 Processing helix chain 'C' and resid 594 through 607 removed outlier: 3.596A pdb=" N LYS C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 removed outlier: 3.761A pdb=" N ALA C 626 " --> pdb=" O PRO C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 630 Processing helix chain 'C' and resid 644 through 652 Processing helix chain 'C' and resid 680 through 682 No H-bonds generated for 'chain 'C' and resid 680 through 682' Processing helix chain 'C' and resid 690 through 707 Processing helix chain 'C' and resid 710 through 721 Processing helix chain 'C' and resid 749 through 762 removed outlier: 3.554A pdb=" N TYR C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL C 756 " --> pdb=" O GLY C 752 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 791 Processing helix chain 'C' and resid 810 through 824 Processing helix chain 'C' and resid 858 through 866 removed outlier: 3.617A pdb=" N ASP C 864 " --> pdb=" O THR C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 870 Processing helix chain 'D' and resid 44 through 51 Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'D' and resid 76 through 91 removed outlier: 3.829A pdb=" N ILE D 80 " --> pdb=" O TYR D 76 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS D 83 " --> pdb=" O HIS D 79 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 86 " --> pdb=" O GLN D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 136 Processing helix chain 'D' and resid 144 through 161 removed outlier: 4.343A pdb=" N ASP D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 Processing helix chain 'D' and resid 194 through 198 Processing helix chain 'D' and resid 210 through 217 Processing helix chain 'D' and resid 219 through 229 Processing helix chain 'D' and resid 245 through 254 removed outlier: 4.309A pdb=" N ASN D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 289 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 405 through 408 removed outlier: 4.067A pdb=" N ILE D 408 " --> pdb=" O THR D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 405 through 408' Processing helix chain 'D' and resid 409 through 424 Processing helix chain 'D' and resid 440 through 445 Processing helix chain 'D' and resid 457 through 462 Processing helix chain 'D' and resid 472 through 480 removed outlier: 3.694A pdb=" N MET D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 512 removed outlier: 3.523A pdb=" N GLN D 512 " --> pdb=" O HIS D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 548 removed outlier: 3.864A pdb=" N VAL D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 568 Processing helix chain 'D' and resid 594 through 607 removed outlier: 3.595A pdb=" N LYS D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 626 removed outlier: 3.761A pdb=" N ALA D 626 " --> pdb=" O PRO D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 630 Processing helix chain 'D' and resid 644 through 652 Processing helix chain 'D' and resid 680 through 682 No H-bonds generated for 'chain 'D' and resid 680 through 682' Processing helix chain 'D' and resid 690 through 707 Processing helix chain 'D' and resid 710 through 721 Processing helix chain 'D' and resid 749 through 762 removed outlier: 3.553A pdb=" N TYR D 753 " --> pdb=" O ASN D 749 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL D 756 " --> pdb=" O GLY D 752 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHE D 759 " --> pdb=" O ALA D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 781 through 791 Processing helix chain 'D' and resid 810 through 824 Processing helix chain 'D' and resid 858 through 866 removed outlier: 3.618A pdb=" N ASP D 864 " --> pdb=" O THR D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 870 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 10 removed outlier: 6.789A pdb=" N ARG A 26 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR A 6 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL A 24 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR A 8 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A 22 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL A 109 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 275 removed outlier: 5.548A pdb=" N ILE A 273 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE A 260 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 403 removed outlier: 4.207A pdb=" N ASP A 307 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 433 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE A 448 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AA6, first strand: chain 'A' and resid 530 through 534 removed outlier: 6.620A pdb=" N ILE A 525 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU A 491 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 490 " --> pdb=" O CYS A 574 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP A 575 " --> pdb=" O TYR A 614 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL A 616 " --> pdb=" O ASP A 575 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY A 577 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ASN A 618 " --> pdb=" O GLY A 577 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N VAL A 579 " --> pdb=" O ASN A 618 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A 635 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N ALA A 658 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR A 637 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N TYR A 660 " --> pdb=" O TYR A 637 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER A 639 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 677 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE A 667 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG A 675 " --> pdb=" O ILE A 667 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU A 669 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N THR A 673 " --> pdb=" O GLU A 669 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 733 through 736 removed outlier: 6.929A pdb=" N HIS A 741 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL A 854 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU A 743 " --> pdb=" O VAL A 854 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE A 768 " --> pdb=" O ARG A 795 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE A 797 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL A 770 " --> pdb=" O ILE A 797 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 2 through 10 removed outlier: 6.789A pdb=" N ARG B 26 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR B 6 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 24 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR B 8 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 22 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL B 109 " --> pdb=" O THR B 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 272 through 275 removed outlier: 5.548A pdb=" N ILE B 273 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ILE B 260 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 400 through 403 removed outlier: 4.207A pdb=" N ASP B 307 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 433 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE B 448 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AB4, first strand: chain 'B' and resid 530 through 534 removed outlier: 6.620A pdb=" N ILE B 525 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 491 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE B 490 " --> pdb=" O CYS B 574 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP B 575 " --> pdb=" O TYR B 614 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL B 616 " --> pdb=" O ASP B 575 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY B 577 " --> pdb=" O VAL B 616 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ASN B 618 " --> pdb=" O GLY B 577 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N VAL B 579 " --> pdb=" O ASN B 618 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL B 635 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N ALA B 658 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR B 637 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N TYR B 660 " --> pdb=" O TYR B 637 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N SER B 639 " --> pdb=" O TYR B 660 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 677 " --> pdb=" O LEU B 665 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B 667 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG B 675 " --> pdb=" O ILE B 667 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU B 669 " --> pdb=" O THR B 673 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N THR B 673 " --> pdb=" O GLU B 669 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 733 through 736 removed outlier: 6.930A pdb=" N HIS B 741 " --> pdb=" O VAL B 852 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL B 854 " --> pdb=" O HIS B 741 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU B 743 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE B 768 " --> pdb=" O ARG B 795 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE B 797 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL B 770 " --> pdb=" O ILE B 797 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 2 through 10 removed outlier: 6.789A pdb=" N ARG C 26 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR C 6 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL C 24 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR C 8 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 22 " --> pdb=" O THR C 8 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL C 109 " --> pdb=" O THR C 104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'C' and resid 272 through 275 removed outlier: 5.548A pdb=" N ILE C 273 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE C 260 " --> pdb=" O ILE C 273 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 400 through 403 removed outlier: 4.207A pdb=" N ASP C 307 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C 433 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE C 448 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AC2, first strand: chain 'C' and resid 530 through 534 removed outlier: 6.620A pdb=" N ILE C 525 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU C 491 " --> pdb=" O LEU C 557 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE C 490 " --> pdb=" O CYS C 574 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP C 575 " --> pdb=" O TYR C 614 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL C 616 " --> pdb=" O ASP C 575 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY C 577 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ASN C 618 " --> pdb=" O GLY C 577 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N VAL C 579 " --> pdb=" O ASN C 618 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL C 635 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N ALA C 658 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR C 637 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N TYR C 660 " --> pdb=" O TYR C 637 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER C 639 " --> pdb=" O TYR C 660 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 677 " --> pdb=" O LEU C 665 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 667 " --> pdb=" O ARG C 675 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG C 675 " --> pdb=" O ILE C 667 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLU C 669 " --> pdb=" O THR C 673 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N THR C 673 " --> pdb=" O GLU C 669 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 733 through 736 removed outlier: 6.929A pdb=" N HIS C 741 " --> pdb=" O VAL C 852 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL C 854 " --> pdb=" O HIS C 741 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU C 743 " --> pdb=" O VAL C 854 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE C 768 " --> pdb=" O ARG C 795 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE C 797 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL C 770 " --> pdb=" O ILE C 797 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 2 through 10 removed outlier: 6.789A pdb=" N ARG D 26 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR D 6 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL D 24 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR D 8 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU D 22 " --> pdb=" O THR D 8 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL D 109 " --> pdb=" O THR D 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'D' and resid 272 through 275 removed outlier: 5.548A pdb=" N ILE D 273 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE D 260 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 400 through 403 removed outlier: 4.207A pdb=" N ASP D 307 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL D 433 " --> pdb=" O ILE D 448 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE D 448 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AC9, first strand: chain 'D' and resid 530 through 534 removed outlier: 6.620A pdb=" N ILE D 525 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU D 491 " --> pdb=" O LEU D 557 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 490 " --> pdb=" O CYS D 574 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP D 575 " --> pdb=" O TYR D 614 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL D 616 " --> pdb=" O ASP D 575 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY D 577 " --> pdb=" O VAL D 616 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ASN D 618 " --> pdb=" O GLY D 577 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N VAL D 579 " --> pdb=" O ASN D 618 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL D 635 " --> pdb=" O ILE D 656 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N ALA D 658 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR D 637 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N TYR D 660 " --> pdb=" O TYR D 637 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER D 639 " --> pdb=" O TYR D 660 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 677 " --> pdb=" O LEU D 665 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE D 667 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG D 675 " --> pdb=" O ILE D 667 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU D 669 " --> pdb=" O THR D 673 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N THR D 673 " --> pdb=" O GLU D 669 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 733 through 736 removed outlier: 6.929A pdb=" N HIS D 741 " --> pdb=" O VAL D 852 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL D 854 " --> pdb=" O HIS D 741 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU D 743 " --> pdb=" O VAL D 854 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE D 768 " --> pdb=" O ARG D 795 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE D 797 " --> pdb=" O PHE D 768 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL D 770 " --> pdb=" O ILE D 797 " (cutoff:3.500A) 1116 hydrogen bonds defined for protein. 3084 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: 5.38 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6029 1.32 - 1.45: 7209 1.45 - 1.58: 14578 1.58 - 1.71: 112 1.71 - 1.84: 160 Bond restraints: 28088 Sorted by residual: bond pdb=" CG GLU B 450 " pdb=" CD GLU B 450 " ideal model delta sigma weight residual 1.516 1.342 0.174 2.50e-02 1.60e+03 4.83e+01 bond pdb=" CG GLU A 450 " pdb=" CD GLU A 450 " ideal model delta sigma weight residual 1.516 1.343 0.173 2.50e-02 1.60e+03 4.80e+01 bond pdb=" CG GLU C 450 " pdb=" CD GLU C 450 " ideal model delta sigma weight residual 1.516 1.343 0.173 2.50e-02 1.60e+03 4.78e+01 bond pdb=" CG GLU D 450 " pdb=" CD GLU D 450 " ideal model delta sigma weight residual 1.516 1.343 0.173 2.50e-02 1.60e+03 4.77e+01 bond pdb=" CB ASN D 528 " pdb=" CG ASN D 528 " ideal model delta sigma weight residual 1.516 1.352 0.164 2.50e-02 1.60e+03 4.28e+01 ... (remaining 28083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.67: 37495 5.67 - 11.34: 633 11.34 - 17.01: 32 17.01 - 22.68: 4 22.68 - 28.35: 12 Bond angle restraints: 38176 Sorted by residual: angle pdb=" PB ATP C 907 " pdb=" O3B ATP C 907 " pdb=" PG ATP C 907 " ideal model delta sigma weight residual 139.87 111.52 28.35 1.00e+00 1.00e+00 8.04e+02 angle pdb=" PB ATP D 907 " pdb=" O3B ATP D 907 " pdb=" PG ATP D 907 " ideal model delta sigma weight residual 139.87 111.55 28.32 1.00e+00 1.00e+00 8.02e+02 angle pdb=" PB ATP A 907 " pdb=" O3B ATP A 907 " pdb=" PG ATP A 907 " ideal model delta sigma weight residual 139.87 111.56 28.31 1.00e+00 1.00e+00 8.02e+02 angle pdb=" PB ATP B 907 " pdb=" O3B ATP B 907 " pdb=" PG ATP B 907 " ideal model delta sigma weight residual 139.87 111.58 28.29 1.00e+00 1.00e+00 8.00e+02 angle pdb=" PB ATP C 906 " pdb=" O3B ATP C 906 " pdb=" PG ATP C 906 " ideal model delta sigma weight residual 139.87 112.55 27.32 1.00e+00 1.00e+00 7.46e+02 ... (remaining 38171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 16541 33.84 - 67.67: 403 67.67 - 101.51: 140 101.51 - 135.35: 60 135.35 - 169.18: 32 Dihedral angle restraints: 17176 sinusoidal: 7144 harmonic: 10032 Sorted by residual: dihedral pdb=" CA 7ID H 1 " pdb=" C 7ID H 1 " pdb=" N 7ID H 2 " pdb=" CA 7ID H 2 " ideal model delta harmonic sigma weight residual -180.00 -70.64 -109.36 0 5.00e+00 4.00e-02 4.78e+02 dihedral pdb=" CA 7ID F 1 " pdb=" C 7ID F 1 " pdb=" N 7ID F 2 " pdb=" CA 7ID F 2 " ideal model delta harmonic sigma weight residual -180.00 -70.66 -109.34 0 5.00e+00 4.00e-02 4.78e+02 dihedral pdb=" CA 7ID G 1 " pdb=" C 7ID G 1 " pdb=" N 7ID G 2 " pdb=" CA 7ID G 2 " ideal model delta harmonic sigma weight residual -180.00 -70.68 -109.32 0 5.00e+00 4.00e-02 4.78e+02 ... (remaining 17173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3008 0.098 - 0.196: 1159 0.196 - 0.294: 179 0.294 - 0.393: 23 0.393 - 0.491: 15 Chirality restraints: 4384 Sorted by residual: chirality pdb=" CA TYR C 256 " pdb=" N TYR C 256 " pdb=" C TYR C 256 " pdb=" CB TYR C 256 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CA TYR A 256 " pdb=" N TYR A 256 " pdb=" C TYR A 256 " pdb=" CB TYR A 256 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" CA TYR B 256 " pdb=" N TYR B 256 " pdb=" C TYR B 256 " pdb=" CB TYR B 256 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.98e+00 ... (remaining 4381 not shown) Planarity restraints: 4988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB 7ID J 2 " -0.090 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" CG 7ID J 2 " 0.086 2.00e-02 2.50e+03 pdb=" OD1 7ID J 2 " -0.179 2.00e-02 2.50e+03 pdb=" CA2 7ID J 2 " -0.349 2.00e-02 2.50e+03 pdb=" N2 7ID J 2 " 0.532 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB 7ID G 3 " -0.147 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" CG 7ID G 3 " 0.093 2.00e-02 2.50e+03 pdb=" OD1 7ID G 3 " -0.128 2.00e-02 2.50e+03 pdb=" CA2 7ID G 3 " -0.351 2.00e-02 2.50e+03 pdb=" N2 7ID G 3 " 0.532 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB 7ID E 3 " -0.147 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" CG 7ID E 3 " 0.093 2.00e-02 2.50e+03 pdb=" OD1 7ID E 3 " -0.128 2.00e-02 2.50e+03 pdb=" CA2 7ID E 3 " -0.351 2.00e-02 2.50e+03 pdb=" N2 7ID E 3 " 0.532 2.00e-02 2.50e+03 ... (remaining 4985 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 60 2.47 - 3.08: 19065 3.08 - 3.69: 40587 3.69 - 4.29: 63762 4.29 - 4.90: 104110 Nonbonded interactions: 227584 Sorted by model distance: nonbonded pdb=" OE2 GLU A 558 " pdb="MG MG A 904 " model vdw 1.865 2.170 nonbonded pdb=" OE2 GLU D 558 " pdb="MG MG D 904 " model vdw 1.865 2.170 nonbonded pdb=" OE2 GLU B 558 " pdb="MG MG B 904 " model vdw 1.865 2.170 nonbonded pdb=" OE2 GLU C 558 " pdb="MG MG C 904 " model vdw 1.865 2.170 nonbonded pdb="MG MG C 904 " pdb=" O1G ATP C 907 " model vdw 1.930 2.170 ... (remaining 227579 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.210 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.150 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.023 0.313 28100 Z= 1.172 Angle : 1.998 28.351 38176 Z= 1.373 Chirality : 0.102 0.491 4384 Planarity : 0.029 0.301 4988 Dihedral : 19.701 169.184 10768 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.16 % Favored : 95.73 % Rotamer: Outliers : 0.70 % Allowed : 0.84 % Favored : 98.45 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.60 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.13), residues: 3464 helix: -1.41 (0.13), residues: 1324 sheet: 0.85 (0.23), residues: 440 loop : -0.22 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 731 TYR 0.052 0.008 TYR D 753 PHE 0.027 0.006 PHE B 43 TRP 0.076 0.011 TRP C 763 HIS 0.011 0.003 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.02197 / 1.16 (28088) covalent geometry : angle 1.99831 / 1.37 (38176) hydrogen bonds : bond 0.20362 / 13.71 ( 1116) hydrogen bonds : angle 7.28350 / 5.06 ( 3084) metal coordination : bond 0.25174 / 15.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 387 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 677 GLU cc_start: 0.7691 (tp30) cc_final: 0.7422 (tp30) REVERT: A 732 MET cc_start: 0.3816 (mtp) cc_final: 0.3587 (pp-130) REVERT: B 152 GLU cc_start: 0.6468 (mt-10) cc_final: 0.6202 (mm-30) REVERT: B 277 HIS cc_start: 0.6426 (m-70) cc_final: 0.6203 (m170) REVERT: B 306 SER cc_start: 0.8696 (m) cc_final: 0.8487 (t) REVERT: B 388 TYR cc_start: 0.7478 (m-80) cc_final: 0.7164 (m-80) REVERT: B 732 MET cc_start: 0.3367 (mtp) cc_final: 0.3055 (pp-130) REVERT: C 152 GLU cc_start: 0.6495 (mt-10) cc_final: 0.6251 (mm-30) REVERT: C 306 SER cc_start: 0.8670 (m) cc_final: 0.8443 (t) REVERT: C 388 TYR cc_start: 0.7540 (m-80) cc_final: 0.7225 (m-80) REVERT: C 732 MET cc_start: 0.3370 (mtp) cc_final: 0.3080 (pp-130) REVERT: D 152 GLU cc_start: 0.6467 (mt-10) cc_final: 0.6184 (mm-30) REVERT: D 306 SER cc_start: 0.8670 (m) cc_final: 0.8449 (t) REVERT: D 388 TYR cc_start: 0.7544 (m-80) cc_final: 0.7214 (m-80) REVERT: D 732 MET cc_start: 0.3320 (mtp) cc_final: 0.3064 (pp-130) outliers start: 20 outliers final: 9 residues processed: 403 average time/residue: 0.7121 time to fit residues: 330.9315 Evaluate side-chains 257 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 248 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PRO Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain B residue 61 PRO Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain C residue 61 PRO Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 61 PRO Chi-restraints excluded: chain D residue 80 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 641 ASN B 541 GLN B 696 ASN C 355 ASN C 541 GLN C 696 ASN D 355 ASN D 541 GLN D 696 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.219013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.142136 restraints weight = 28516.127| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.60 r_work: 0.3327 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28100 Z= 0.165 Angle : 0.793 11.770 38176 Z= 0.397 Chirality : 0.051 0.280 4384 Planarity : 0.005 0.049 4988 Dihedral : 25.312 179.717 4563 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.18 % Allowed : 5.94 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3464 helix: -0.04 (0.14), residues: 1316 sheet: 1.17 (0.24), residues: 488 loop : -0.66 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 100 TYR 0.015 0.002 TYR A 76 PHE 0.020 0.002 PHE A 43 TRP 0.010 0.002 TRP A 763 HIS 0.006 0.001 HIS B 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (28088) covalent geometry : angle 0.79328 / 0.40 (38176) hydrogen bonds : bond 0.05353 / 3.54 ( 1116) hydrogen bonds : angle 5.01417 / 3.50 ( 3084) metal coordination : bond 0.01764 / 1.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 303 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8167 (mpp-170) cc_final: 0.7754 (mtp180) REVERT: A 64 GLN cc_start: 0.7124 (tm-30) cc_final: 0.6875 (tm-30) REVERT: A 236 ARG cc_start: 0.7152 (ttm-80) cc_final: 0.6674 (ttp-170) REVERT: A 586 HIS cc_start: 0.7901 (m90) cc_final: 0.7656 (m90) REVERT: A 722 THR cc_start: 0.7698 (p) cc_final: 0.7478 (t) REVERT: A 732 MET cc_start: 0.3708 (mtp) cc_final: 0.3193 (pp-130) REVERT: B 18 ARG cc_start: 0.8299 (mpp-170) cc_final: 0.7761 (mtp180) REVERT: B 155 ARG cc_start: 0.6691 (mtt90) cc_final: 0.6327 (mtt90) REVERT: B 286 ASP cc_start: 0.8212 (m-30) cc_final: 0.7946 (m-30) REVERT: B 306 SER cc_start: 0.8868 (m) cc_final: 0.8603 (t) REVERT: B 459 MET cc_start: 0.8724 (ptm) cc_final: 0.8408 (ptm) REVERT: B 558 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: B 661 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7672 (pt0) REVERT: B 722 THR cc_start: 0.7711 (p) cc_final: 0.7423 (t) REVERT: B 732 MET cc_start: 0.3432 (mtp) cc_final: 0.2923 (pp-130) REVERT: C 18 ARG cc_start: 0.8290 (mpp-170) cc_final: 0.7754 (mtp180) REVERT: C 155 ARG cc_start: 0.6750 (mtt90) cc_final: 0.6393 (mtt90) REVERT: C 286 ASP cc_start: 0.8275 (m-30) cc_final: 0.8015 (m-30) REVERT: C 306 SER cc_start: 0.8888 (m) cc_final: 0.8600 (t) REVERT: C 387 VAL cc_start: 0.7963 (t) cc_final: 0.7659 (p) REVERT: C 459 MET cc_start: 0.8700 (ptm) cc_final: 0.8398 (ptm) REVERT: C 558 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: C 661 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7623 (pt0) REVERT: C 722 THR cc_start: 0.7777 (p) cc_final: 0.7495 (t) REVERT: C 732 MET cc_start: 0.3353 (mtp) cc_final: 0.2899 (pp-130) REVERT: D 18 ARG cc_start: 0.8272 (mpp-170) cc_final: 0.7738 (mtp180) REVERT: D 155 ARG cc_start: 0.6678 (mtt90) cc_final: 0.6352 (mtt90) REVERT: D 219 ASP cc_start: 0.8242 (t0) cc_final: 0.8005 (t0) REVERT: D 286 ASP cc_start: 0.8285 (m-30) cc_final: 0.8030 (m-30) REVERT: D 306 SER cc_start: 0.8940 (m) cc_final: 0.8669 (t) REVERT: D 387 VAL cc_start: 0.7965 (t) cc_final: 0.7669 (p) REVERT: D 459 MET cc_start: 0.8726 (ptm) cc_final: 0.8427 (ptm) REVERT: D 558 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: D 661 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7868 (pp20) REVERT: D 677 GLU cc_start: 0.8365 (tp30) cc_final: 0.8163 (tp30) REVERT: D 722 THR cc_start: 0.7712 (p) cc_final: 0.7441 (t) REVERT: D 732 MET cc_start: 0.3409 (mtp) cc_final: 0.2912 (pp-130) outliers start: 62 outliers final: 15 residues processed: 333 average time/residue: 0.6481 time to fit residues: 253.2713 Evaluate side-chains 281 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 260 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 661 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 284 optimal weight: 4.9990 chunk 339 optimal weight: 20.0000 chunk 272 optimal weight: 3.9990 chunk 302 optimal weight: 0.5980 chunk 174 optimal weight: 5.9990 chunk 233 optimal weight: 0.0470 chunk 243 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 63 optimal weight: 0.0770 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN A 696 ASN C 541 GLN D 541 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.216559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.133843 restraints weight = 28459.321| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.17 r_work: 0.3269 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28100 Z= 0.138 Angle : 0.655 11.505 38176 Z= 0.332 Chirality : 0.047 0.257 4384 Planarity : 0.004 0.043 4988 Dihedral : 24.469 178.646 4540 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.62 % Allowed : 8.23 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3464 helix: 0.40 (0.15), residues: 1324 sheet: 1.14 (0.23), residues: 508 loop : -0.74 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 469 TYR 0.015 0.002 TYR A 519 PHE 0.014 0.002 PHE B 692 TRP 0.007 0.001 TRP A 414 HIS 0.005 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (28088) covalent geometry : angle 0.65541 / 0.33 (38176) hydrogen bonds : bond 0.04566 / 3.04 ( 1116) hydrogen bonds : angle 4.61106 / 3.23 ( 3084) metal coordination : bond 0.01329 / 0.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 295 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.7149 (tm-30) cc_final: 0.6859 (tm-30) REVERT: A 102 ARG cc_start: 0.7401 (mmt-90) cc_final: 0.6613 (mmp80) REVERT: A 236 ARG cc_start: 0.7247 (ttm-80) cc_final: 0.6768 (ttp-170) REVERT: A 558 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: A 732 MET cc_start: 0.3989 (mtp) cc_final: 0.3459 (pmt) REVERT: B 18 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7812 (mpp-170) REVERT: B 64 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.6934 (tm-30) REVERT: B 155 ARG cc_start: 0.6828 (mtt90) cc_final: 0.6498 (mtt90) REVERT: B 286 ASP cc_start: 0.8255 (m-30) cc_final: 0.8032 (m-30) REVERT: B 632 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8186 (tmmt) REVERT: B 732 MET cc_start: 0.3628 (mtp) cc_final: 0.2906 (pp-130) REVERT: C 64 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.6937 (tm-30) REVERT: C 155 ARG cc_start: 0.6649 (mtt90) cc_final: 0.6315 (mtt90) REVERT: C 286 ASP cc_start: 0.8300 (m-30) cc_final: 0.8078 (m-30) REVERT: C 355 ASN cc_start: 0.8075 (t0) cc_final: 0.7859 (t0) REVERT: C 387 VAL cc_start: 0.8103 (t) cc_final: 0.7870 (p) REVERT: C 632 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8153 (tmmt) REVERT: C 732 MET cc_start: 0.3629 (mtp) cc_final: 0.2932 (pp-130) REVERT: D 18 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7790 (mpp-170) REVERT: D 64 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.6918 (tm-30) REVERT: D 155 ARG cc_start: 0.6597 (mtt90) cc_final: 0.6261 (mtt90) REVERT: D 236 ARG cc_start: 0.7146 (ttt90) cc_final: 0.6934 (ttp-170) REVERT: D 286 ASP cc_start: 0.8323 (m-30) cc_final: 0.8104 (m-30) REVERT: D 355 ASN cc_start: 0.8072 (t0) cc_final: 0.7839 (t0) REVERT: D 387 VAL cc_start: 0.8098 (t) cc_final: 0.7859 (p) REVERT: D 632 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8187 (tmmt) REVERT: D 732 MET cc_start: 0.3643 (mtp) cc_final: 0.2921 (pp-130) outliers start: 46 outliers final: 12 residues processed: 323 average time/residue: 0.6498 time to fit residues: 246.4245 Evaluate side-chains 270 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 632 LYS Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 632 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 94 optimal weight: 6.9990 chunk 299 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 233 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 318 optimal weight: 0.3980 chunk 155 optimal weight: 0.0010 chunk 58 optimal weight: 0.0170 chunk 209 optimal weight: 6.9990 overall best weight: 0.8226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN B 202 GLN C 202 GLN D 202 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.216131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137112 restraints weight = 27951.947| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.62 r_work: 0.3283 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28100 Z= 0.127 Angle : 0.618 10.944 38176 Z= 0.313 Chirality : 0.046 0.226 4384 Planarity : 0.004 0.050 4988 Dihedral : 23.676 170.922 4540 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.26 % Favored : 96.62 % Rotamer: Outliers : 2.22 % Allowed : 8.90 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.14), residues: 3464 helix: 0.52 (0.15), residues: 1320 sheet: 0.61 (0.24), residues: 440 loop : -0.80 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 469 TYR 0.016 0.002 TYR A 519 PHE 0.015 0.002 PHE D 692 TRP 0.007 0.001 TRP A 414 HIS 0.004 0.001 HIS B 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (28088) covalent geometry : angle 0.61769 / 0.31 (38176) hydrogen bonds : bond 0.04305 / 2.86 ( 1116) hydrogen bonds : angle 4.47739 / 3.14 ( 3084) metal coordination : bond 0.00535 / 0.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 271 time to evaluate : 0.910 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 18 ARG cc_start: 0.8213 (mpp-170) cc_final: 0.7795 (mtp180) REVERT: A 64 GLN cc_start: 0.7305 (tm-30) cc_final: 0.6983 (tm-30) REVERT: A 236 ARG cc_start: 0.7291 (ttm-80) cc_final: 0.6833 (ttp-170) REVERT: A 558 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: A 732 MET cc_start: 0.3771 (mtp) cc_final: 0.3104 (pp-130) REVERT: B 64 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7006 (tm-30) REVERT: B 151 LEU cc_start: 0.6940 (mm) cc_final: 0.6383 (tp) REVERT: B 155 ARG cc_start: 0.6773 (mtt90) cc_final: 0.6557 (mtt90) REVERT: B 160 ASN cc_start: 0.8071 (t0) cc_final: 0.7739 (t0) REVERT: B 236 ARG cc_start: 0.7319 (ttt180) cc_final: 0.7053 (ttp-170) REVERT: B 286 ASP cc_start: 0.8345 (m-30) cc_final: 0.8111 (m-30) REVERT: B 444 THR cc_start: 0.8449 (p) cc_final: 0.8133 (m) REVERT: B 558 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: B 632 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8167 (tmmt) REVERT: B 684 MET cc_start: 0.8826 (ptm) cc_final: 0.8522 (ttt) REVERT: B 732 MET cc_start: 0.3530 (mtp) cc_final: 0.2913 (pp-130) REVERT: C 18 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7796 (mtp180) REVERT: C 64 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7055 (tm-30) REVERT: C 151 LEU cc_start: 0.6821 (mm) cc_final: 0.6349 (tp) REVERT: C 286 ASP cc_start: 0.8386 (m-30) cc_final: 0.8150 (m-30) REVERT: C 355 ASN cc_start: 0.8147 (t0) cc_final: 0.7923 (t0) REVERT: C 444 THR cc_start: 0.8430 (p) cc_final: 0.8109 (m) REVERT: C 558 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: C 684 MET cc_start: 0.8822 (ptm) cc_final: 0.8513 (ttt) REVERT: C 732 MET cc_start: 0.3485 (mtp) cc_final: 0.2881 (pp-130) REVERT: D 18 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7801 (mtp180) REVERT: D 64 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7003 (tm-30) REVERT: D 151 LEU cc_start: 0.6818 (mm) cc_final: 0.6331 (tp) REVERT: D 286 ASP cc_start: 0.8417 (m-30) cc_final: 0.8182 (m-30) REVERT: D 355 ASN cc_start: 0.8150 (t0) cc_final: 0.7915 (t0) REVERT: D 387 VAL cc_start: 0.8092 (t) cc_final: 0.7836 (p) REVERT: D 444 THR cc_start: 0.8440 (p) cc_final: 0.8127 (m) REVERT: D 558 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: D 632 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8151 (tmmt) REVERT: D 684 MET cc_start: 0.8851 (ptm) cc_final: 0.8550 (ttt) REVERT: D 732 MET cc_start: 0.3493 (mtp) cc_final: 0.2902 (pp-130) outliers start: 63 outliers final: 26 residues processed: 314 average time/residue: 0.5960 time to fit residues: 219.4296 Evaluate side-chains 285 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 248 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 737 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 144 optimal weight: 3.9990 chunk 169 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 206 optimal weight: 0.3980 chunk 225 optimal weight: 4.9990 chunk 312 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 707 ASN B 586 HIS B 707 ASN C 160 ASN C 707 ASN D 160 ASN D 707 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.212213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.130316 restraints weight = 27847.148| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.14 r_work: 0.3188 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 28100 Z= 0.208 Angle : 0.688 10.859 38176 Z= 0.356 Chirality : 0.049 0.228 4384 Planarity : 0.005 0.044 4988 Dihedral : 23.461 163.029 4540 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.81 % Favored : 96.07 % Rotamer: Outliers : 2.18 % Allowed : 10.20 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.14), residues: 3464 helix: 0.23 (0.14), residues: 1332 sheet: 0.49 (0.24), residues: 432 loop : -1.06 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 469 TYR 0.022 0.002 TYR B 116 PHE 0.029 0.003 PHE C 692 TRP 0.009 0.002 TRP A 414 HIS 0.005 0.001 HIS D 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 (28088) covalent geometry : angle 0.68763 / 0.36 (38176) hydrogen bonds : bond 0.05799 / 3.91 ( 1116) hydrogen bonds : angle 4.70154 / 3.29 ( 3084) metal coordination : bond 0.01124 / 0.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 262 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8332 (mpp-170) cc_final: 0.7908 (mtp180) REVERT: A 64 GLN cc_start: 0.7422 (tm-30) cc_final: 0.7118 (tm-30) REVERT: A 558 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: A 732 MET cc_start: 0.4269 (mtp) cc_final: 0.3315 (pp-130) REVERT: A 737 LEU cc_start: 0.0886 (OUTLIER) cc_final: 0.0494 (tp) REVERT: B 18 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7844 (mtp180) REVERT: B 64 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.6997 (tm-30) REVERT: B 151 LEU cc_start: 0.6942 (mm) cc_final: 0.6385 (tp) REVERT: B 160 ASN cc_start: 0.8060 (t0) cc_final: 0.7741 (t0) REVERT: B 221 GLU cc_start: 0.8270 (mp0) cc_final: 0.7973 (mp0) REVERT: B 236 ARG cc_start: 0.7441 (ttt180) cc_final: 0.7217 (ttp-170) REVERT: B 444 THR cc_start: 0.8383 (p) cc_final: 0.8074 (m) REVERT: B 558 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: B 732 MET cc_start: 0.3986 (mtp) cc_final: 0.2975 (pp-130) REVERT: B 737 LEU cc_start: 0.0683 (OUTLIER) cc_final: -0.0174 (tp) REVERT: C 1 MET cc_start: 0.8427 (mtp) cc_final: 0.8209 (mtt) REVERT: C 18 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7821 (mtp180) REVERT: C 64 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.6942 (tm-30) REVERT: C 151 LEU cc_start: 0.6934 (mm) cc_final: 0.6384 (tp) REVERT: C 160 ASN cc_start: 0.8001 (t0) cc_final: 0.7679 (t0) REVERT: C 444 THR cc_start: 0.8350 (p) cc_final: 0.8046 (m) REVERT: C 558 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: C 732 MET cc_start: 0.3997 (mtp) cc_final: 0.3129 (pmt) REVERT: D 18 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7843 (mpp-170) REVERT: D 64 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.6980 (tm-30) REVERT: D 151 LEU cc_start: 0.6943 (mm) cc_final: 0.6390 (tp) REVERT: D 160 ASN cc_start: 0.7982 (t0) cc_final: 0.7660 (t0) REVERT: D 444 THR cc_start: 0.8349 (p) cc_final: 0.8058 (m) REVERT: D 558 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: D 732 MET cc_start: 0.4056 (mtp) cc_final: 0.3031 (pp-130) REVERT: D 737 LEU cc_start: 0.0648 (OUTLIER) cc_final: -0.0102 (tp) outliers start: 62 outliers final: 27 residues processed: 305 average time/residue: 0.6118 time to fit residues: 220.9396 Evaluate side-chains 290 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 250 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 737 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 70 optimal weight: 0.8980 chunk 347 optimal weight: 3.9990 chunk 304 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 292 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 275 optimal weight: 2.9990 chunk 263 optimal weight: 4.9990 chunk 294 optimal weight: 0.0570 chunk 308 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 541 GLN D 740 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.215063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.134843 restraints weight = 27799.910| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.34 r_work: 0.3224 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28100 Z= 0.114 Angle : 0.588 10.768 38176 Z= 0.300 Chirality : 0.045 0.205 4384 Planarity : 0.004 0.048 4988 Dihedral : 22.896 159.699 4540 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.55 % Favored : 96.33 % Rotamer: Outliers : 1.58 % Allowed : 11.15 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.14), residues: 3464 helix: 0.38 (0.15), residues: 1332 sheet: 0.41 (0.21), residues: 600 loop : -1.09 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 26 TYR 0.014 0.001 TYR B 63 PHE 0.014 0.002 PHE A 692 TRP 0.006 0.001 TRP A 414 HIS 0.027 0.001 HIS B 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (28088) covalent geometry : angle 0.58786 / 0.30 (38176) hydrogen bonds : bond 0.04160 / 2.77 ( 1116) hydrogen bonds : angle 4.49862 / 3.16 ( 3084) metal coordination : bond 0.00404 / 0.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 254 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8348 (mpp-170) cc_final: 0.7893 (mtp180) REVERT: A 558 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: A 732 MET cc_start: 0.3985 (mtp) cc_final: 0.3357 (pp-130) REVERT: A 737 LEU cc_start: 0.0892 (OUTLIER) cc_final: 0.0685 (tp) REVERT: B 18 ARG cc_start: 0.8354 (mpp-170) cc_final: 0.7865 (mtp180) REVERT: B 64 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7017 (tm-30) REVERT: B 151 LEU cc_start: 0.6864 (mm) cc_final: 0.6359 (tp) REVERT: B 160 ASN cc_start: 0.8026 (t0) cc_final: 0.7697 (t0) REVERT: B 221 GLU cc_start: 0.8184 (mp0) cc_final: 0.7928 (mp0) REVERT: B 236 ARG cc_start: 0.7396 (ttt180) cc_final: 0.7166 (ttp-170) REVERT: B 558 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: B 684 MET cc_start: 0.8860 (ptm) cc_final: 0.8573 (ttt) REVERT: B 732 MET cc_start: 0.3670 (mtp) cc_final: 0.2985 (pp-130) REVERT: B 737 LEU cc_start: 0.0645 (OUTLIER) cc_final: -0.0012 (tp) REVERT: C 18 ARG cc_start: 0.8346 (mpp-170) cc_final: 0.7891 (mtp180) REVERT: C 64 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: C 151 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6306 (tp) REVERT: C 221 GLU cc_start: 0.8132 (mp0) cc_final: 0.7884 (mp0) REVERT: C 355 ASN cc_start: 0.8024 (t0) cc_final: 0.7811 (t0) REVERT: C 558 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: C 684 MET cc_start: 0.8840 (ptm) cc_final: 0.8558 (ttt) REVERT: C 732 MET cc_start: 0.3672 (mtp) cc_final: 0.3008 (pp-130) REVERT: C 737 LEU cc_start: 0.0623 (OUTLIER) cc_final: -0.0172 (tp) REVERT: D 18 ARG cc_start: 0.8378 (mpp-170) cc_final: 0.7894 (mtp180) REVERT: D 64 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: D 151 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6295 (tp) REVERT: D 221 GLU cc_start: 0.8154 (mp0) cc_final: 0.7910 (mp0) REVERT: D 355 ASN cc_start: 0.8065 (t0) cc_final: 0.7848 (t0) REVERT: D 558 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: D 732 MET cc_start: 0.3845 (mtp) cc_final: 0.3111 (pp-130) outliers start: 45 outliers final: 25 residues processed: 287 average time/residue: 0.6259 time to fit residues: 211.4480 Evaluate side-chains 275 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 711 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 111 optimal weight: 4.9990 chunk 253 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 30.0000 chunk 26 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 ASN D 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.211397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130645 restraints weight = 27690.764| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.55 r_work: 0.3159 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 28100 Z= 0.215 Angle : 0.686 9.652 38176 Z= 0.356 Chirality : 0.050 0.212 4384 Planarity : 0.005 0.045 4988 Dihedral : 22.938 159.809 4540 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.90 % Favored : 95.99 % Rotamer: Outliers : 2.07 % Allowed : 11.15 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.14), residues: 3464 helix: 0.12 (0.14), residues: 1340 sheet: 0.28 (0.24), residues: 432 loop : -1.19 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 715 TYR 0.022 0.002 TYR A 116 PHE 0.031 0.003 PHE D 692 TRP 0.009 0.002 TRP D 414 HIS 0.004 0.001 HIS D 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.21 (28088) covalent geometry : angle 0.68580 / 0.36 (38176) hydrogen bonds : bond 0.05930 / 4.00 ( 1116) hydrogen bonds : angle 4.75018 / 3.33 ( 3084) metal coordination : bond 0.00988 / 0.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 254 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8412 (mpp-170) cc_final: 0.7952 (mtp180) REVERT: A 558 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: A 732 MET cc_start: 0.4469 (mtp) cc_final: 0.3454 (pp-130) REVERT: A 737 LEU cc_start: 0.1006 (OUTLIER) cc_final: 0.0758 (tp) REVERT: B 18 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7959 (mtm110) REVERT: B 64 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.6991 (tm-30) REVERT: B 151 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6386 (tp) REVERT: B 160 ASN cc_start: 0.8104 (t0) cc_final: 0.7786 (t0) REVERT: B 221 GLU cc_start: 0.8360 (mp0) cc_final: 0.8092 (mp0) REVERT: B 236 ARG cc_start: 0.7548 (ttt180) cc_final: 0.7326 (ttp-170) REVERT: B 558 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: B 732 MET cc_start: 0.4270 (mtp) cc_final: 0.3530 (pmt) REVERT: B 737 LEU cc_start: 0.0735 (OUTLIER) cc_final: 0.0016 (tp) REVERT: C 18 ARG cc_start: 0.8383 (mpp-170) cc_final: 0.7932 (mtm110) REVERT: C 64 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.6998 (tm-30) REVERT: C 151 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6292 (tp) REVERT: C 160 ASN cc_start: 0.8054 (t0) cc_final: 0.7769 (t0) REVERT: C 221 GLU cc_start: 0.8293 (mp0) cc_final: 0.8077 (mp0) REVERT: C 355 ASN cc_start: 0.8112 (t0) cc_final: 0.7880 (t0) REVERT: C 558 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: C 732 MET cc_start: 0.4373 (mtp) cc_final: 0.3731 (pmt) REVERT: C 737 LEU cc_start: 0.0643 (OUTLIER) cc_final: -0.0253 (tp) REVERT: D 18 ARG cc_start: 0.8419 (mpp-170) cc_final: 0.7964 (mtm110) REVERT: D 64 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: D 151 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6303 (tp) REVERT: D 160 ASN cc_start: 0.8052 (t0) cc_final: 0.7779 (t0) REVERT: D 221 GLU cc_start: 0.8294 (mp0) cc_final: 0.8055 (mp0) REVERT: D 236 ARG cc_start: 0.7721 (ttp-170) cc_final: 0.7391 (ttt180) REVERT: D 355 ASN cc_start: 0.8093 (t0) cc_final: 0.7840 (t0) REVERT: D 558 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: D 732 MET cc_start: 0.4254 (mtp) cc_final: 0.3244 (pp-130) REVERT: D 737 LEU cc_start: 0.0719 (OUTLIER) cc_final: 0.0062 (tp) outliers start: 59 outliers final: 28 residues processed: 292 average time/residue: 0.5995 time to fit residues: 207.9772 Evaluate side-chains 294 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 630 LYS Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 737 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 276 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 304 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 281 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 740 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.213951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.133555 restraints weight = 27829.276| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.36 r_work: 0.3198 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28100 Z= 0.128 Angle : 0.596 9.059 38176 Z= 0.306 Chirality : 0.046 0.196 4384 Planarity : 0.004 0.051 4988 Dihedral : 22.444 160.955 4540 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.81 % Favored : 96.07 % Rotamer: Outliers : 1.72 % Allowed : 11.74 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.14), residues: 3464 helix: 0.32 (0.15), residues: 1324 sheet: 0.18 (0.21), residues: 596 loop : -1.21 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 26 TYR 0.024 0.002 TYR A 256 PHE 0.014 0.002 PHE C 692 TRP 0.011 0.001 TRP B 278 HIS 0.004 0.001 HIS C 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (28088) covalent geometry : angle 0.59623 / 0.31 (38176) hydrogen bonds : bond 0.04374 / 2.92 ( 1116) hydrogen bonds : angle 4.54710 / 3.20 ( 3084) metal coordination : bond 0.00494 / 0.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 253 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8389 (mpp-170) cc_final: 0.7951 (mtm110) REVERT: A 236 ARG cc_start: 0.7515 (ttp-170) cc_final: 0.6889 (ptm160) REVERT: A 558 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: A 732 MET cc_start: 0.4253 (mtp) cc_final: 0.3356 (pp-130) REVERT: A 737 LEU cc_start: 0.1063 (OUTLIER) cc_final: 0.0852 (tp) REVERT: B 18 ARG cc_start: 0.8415 (mpp-170) cc_final: 0.8002 (mtm110) REVERT: B 64 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.6990 (tm-30) REVERT: B 151 LEU cc_start: 0.6873 (mm) cc_final: 0.6334 (tp) REVERT: B 160 ASN cc_start: 0.8075 (t0) cc_final: 0.7748 (t0) REVERT: B 221 GLU cc_start: 0.8205 (mp0) cc_final: 0.7975 (mp0) REVERT: B 236 ARG cc_start: 0.7456 (ttt180) cc_final: 0.7229 (ttp-170) REVERT: B 558 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: B 627 MET cc_start: 0.8520 (mtt) cc_final: 0.8202 (mtm) REVERT: B 684 MET cc_start: 0.8843 (ptm) cc_final: 0.8546 (ttt) REVERT: B 732 MET cc_start: 0.4143 (mtp) cc_final: 0.3026 (pp-130) REVERT: B 737 LEU cc_start: 0.0856 (OUTLIER) cc_final: 0.0180 (tp) REVERT: C 18 ARG cc_start: 0.8408 (mpp-170) cc_final: 0.7978 (mtm110) REVERT: C 64 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: C 151 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6185 (tp) REVERT: C 160 ASN cc_start: 0.8050 (t0) cc_final: 0.7774 (t0) REVERT: C 236 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7353 (ttt180) REVERT: C 355 ASN cc_start: 0.8087 (t0) cc_final: 0.7866 (t0) REVERT: C 558 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: C 684 MET cc_start: 0.8856 (ptm) cc_final: 0.8594 (ttt) REVERT: C 732 MET cc_start: 0.4240 (mtp) cc_final: 0.3479 (pmt) REVERT: C 737 LEU cc_start: 0.0669 (OUTLIER) cc_final: -0.0185 (tp) REVERT: D 1 MET cc_start: 0.8190 (mtt) cc_final: 0.7973 (mtt) REVERT: D 18 ARG cc_start: 0.8429 (mpp-170) cc_final: 0.8007 (mtm110) REVERT: D 64 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: D 151 LEU cc_start: 0.6742 (mm) cc_final: 0.6195 (tp) REVERT: D 160 ASN cc_start: 0.8042 (t0) cc_final: 0.7766 (t0) REVERT: D 221 GLU cc_start: 0.8186 (mp0) cc_final: 0.7975 (mp0) REVERT: D 236 ARG cc_start: 0.7648 (ttp-170) cc_final: 0.7299 (ttt180) REVERT: D 355 ASN cc_start: 0.8143 (t0) cc_final: 0.7907 (t0) REVERT: D 558 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: D 684 MET cc_start: 0.8874 (ptm) cc_final: 0.8614 (ttt) REVERT: D 732 MET cc_start: 0.4142 (mtp) cc_final: 0.3176 (pp-130) REVERT: D 737 LEU cc_start: 0.0726 (OUTLIER) cc_final: 0.0182 (tp) outliers start: 49 outliers final: 26 residues processed: 292 average time/residue: 0.6085 time to fit residues: 210.6885 Evaluate side-chains 286 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 630 LYS Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 737 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 80 optimal weight: 50.0000 chunk 244 optimal weight: 0.6980 chunk 232 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 281 optimal weight: 1.9990 chunk 198 optimal weight: 8.9990 chunk 273 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.211332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130170 restraints weight = 27856.490| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.38 r_work: 0.3157 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28100 Z= 0.209 Angle : 0.676 8.614 38176 Z= 0.351 Chirality : 0.049 0.200 4384 Planarity : 0.005 0.048 4988 Dihedral : 22.577 162.454 4540 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.87 % Favored : 96.02 % Rotamer: Outliers : 1.93 % Allowed : 11.39 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.14), residues: 3464 helix: 0.15 (0.14), residues: 1332 sheet: 0.30 (0.24), residues: 412 loop : -1.31 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 469 TYR 0.023 0.002 TYR A 256 PHE 0.029 0.003 PHE D 692 TRP 0.009 0.002 TRP B 414 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (28088) covalent geometry : angle 0.67645 / 0.35 (38176) hydrogen bonds : bond 0.05799 / 3.91 ( 1116) hydrogen bonds : angle 4.76143 / 3.34 ( 3084) metal coordination : bond 0.01076 / 0.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8407 (mpp-170) cc_final: 0.7972 (mtm110) REVERT: A 236 ARG cc_start: 0.7664 (ttp-170) cc_final: 0.7052 (ptm160) REVERT: A 558 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: A 627 MET cc_start: 0.8551 (mtt) cc_final: 0.8203 (mtm) REVERT: B 18 ARG cc_start: 0.8422 (mpp-170) cc_final: 0.8004 (mtm110) REVERT: B 64 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7029 (tm-30) REVERT: B 151 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6353 (tp) REVERT: B 160 ASN cc_start: 0.8100 (t0) cc_final: 0.7806 (t0) REVERT: B 221 GLU cc_start: 0.8335 (mp0) cc_final: 0.8098 (mp0) REVERT: B 236 ARG cc_start: 0.7526 (ttt180) cc_final: 0.7319 (ttp-170) REVERT: B 558 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: B 732 MET cc_start: 0.4462 (mtp) cc_final: 0.3785 (pmt) REVERT: B 737 LEU cc_start: 0.0831 (OUTLIER) cc_final: 0.0127 (tp) REVERT: C 1 MET cc_start: 0.8180 (mtt) cc_final: 0.7901 (mtt) REVERT: C 18 ARG cc_start: 0.8368 (mpp-170) cc_final: 0.7962 (mtm110) REVERT: C 64 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7005 (tm-30) REVERT: C 151 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6224 (tp) REVERT: C 160 ASN cc_start: 0.8034 (t0) cc_final: 0.7774 (t0) REVERT: C 355 ASN cc_start: 0.8108 (t0) cc_final: 0.7839 (t0) REVERT: C 558 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: C 732 MET cc_start: 0.4440 (mtp) cc_final: 0.3399 (pp-130) REVERT: C 737 LEU cc_start: 0.0835 (OUTLIER) cc_final: -0.0057 (tp) REVERT: D 18 ARG cc_start: 0.8443 (mpp-170) cc_final: 0.8030 (mtm110) REVERT: D 64 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7004 (tm-30) REVERT: D 151 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6279 (tp) REVERT: D 160 ASN cc_start: 0.8041 (t0) cc_final: 0.7784 (t0) REVERT: D 221 GLU cc_start: 0.8300 (mp0) cc_final: 0.8078 (mp0) REVERT: D 355 ASN cc_start: 0.8192 (t0) cc_final: 0.7894 (t0) REVERT: D 558 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: D 732 MET cc_start: 0.4471 (mtp) cc_final: 0.3414 (pp-130) REVERT: D 737 LEU cc_start: 0.0834 (OUTLIER) cc_final: 0.0179 (tp) outliers start: 55 outliers final: 32 residues processed: 286 average time/residue: 0.5934 time to fit residues: 201.7542 Evaluate side-chains 284 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 239 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 630 LYS Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 630 LYS Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 737 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 275 optimal weight: 6.9990 chunk 343 optimal weight: 20.0000 chunk 185 optimal weight: 0.7980 chunk 258 optimal weight: 3.9990 chunk 286 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.213536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148317 restraints weight = 27914.099| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.60 r_work: 0.3280 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 28100 Z= 0.127 Angle : 0.594 10.039 38176 Z= 0.305 Chirality : 0.046 0.189 4384 Planarity : 0.004 0.054 4988 Dihedral : 22.166 166.054 4540 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.72 % Favored : 96.16 % Rotamer: Outliers : 1.79 % Allowed : 11.74 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.14), residues: 3464 helix: 0.23 (0.15), residues: 1352 sheet: 0.18 (0.22), residues: 592 loop : -1.23 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 869 TYR 0.027 0.002 TYR D 256 PHE 0.014 0.002 PHE D 692 TRP 0.008 0.001 TRP A 181 HIS 0.006 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (28088) covalent geometry : angle 0.59423 / 0.31 (38176) hydrogen bonds : bond 0.04351 / 2.91 ( 1116) hydrogen bonds : angle 4.59258 / 3.23 ( 3084) metal coordination : bond 0.00497 / 0.30 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 248 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8342 (mpp-170) cc_final: 0.8073 (mtm110) REVERT: A 236 ARG cc_start: 0.7544 (ttp-170) cc_final: 0.7115 (ptm160) REVERT: A 379 SER cc_start: 0.7261 (t) cc_final: 0.6772 (p) REVERT: A 558 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: A 732 MET cc_start: 0.4114 (ptp) cc_final: 0.3618 (pp-130) REVERT: B 18 ARG cc_start: 0.8352 (mpp-170) cc_final: 0.8116 (mtm110) REVERT: B 64 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: B 151 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6554 (tp) REVERT: B 160 ASN cc_start: 0.8129 (t0) cc_final: 0.7833 (t0) REVERT: B 221 GLU cc_start: 0.8276 (mp0) cc_final: 0.8068 (mp0) REVERT: B 558 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: B 684 MET cc_start: 0.8811 (ptm) cc_final: 0.8528 (ttt) REVERT: B 732 MET cc_start: 0.4260 (mtp) cc_final: 0.3498 (pp-130) REVERT: B 737 LEU cc_start: 0.0683 (OUTLIER) cc_final: 0.0203 (tp) REVERT: C 1 MET cc_start: 0.8068 (mtt) cc_final: 0.7748 (mtt) REVERT: C 18 ARG cc_start: 0.8349 (mpp-170) cc_final: 0.8136 (mtm110) REVERT: C 64 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: C 151 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6477 (tp) REVERT: C 160 ASN cc_start: 0.8112 (t0) cc_final: 0.7843 (t0) REVERT: C 236 ARG cc_start: 0.7740 (ttp-170) cc_final: 0.7462 (ptm160) REVERT: C 355 ASN cc_start: 0.8171 (t0) cc_final: 0.7968 (t0) REVERT: C 558 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: C 684 MET cc_start: 0.8829 (ptm) cc_final: 0.8551 (ttt) REVERT: C 732 MET cc_start: 0.4235 (mtp) cc_final: 0.3436 (pp-130) REVERT: C 737 LEU cc_start: 0.0546 (OUTLIER) cc_final: -0.0103 (tp) REVERT: D 18 ARG cc_start: 0.8385 (mpp-170) cc_final: 0.8168 (mtm110) REVERT: D 64 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: D 151 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6481 (tp) REVERT: D 160 ASN cc_start: 0.8154 (t0) cc_final: 0.7880 (t0) REVERT: D 355 ASN cc_start: 0.8183 (t0) cc_final: 0.7967 (t0) REVERT: D 558 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: D 684 MET cc_start: 0.8841 (ptm) cc_final: 0.8608 (ttt) REVERT: D 732 MET cc_start: 0.4310 (mtp) cc_final: 0.3601 (pp-130) REVERT: D 737 LEU cc_start: 0.0480 (OUTLIER) cc_final: 0.0073 (tp) outliers start: 51 outliers final: 28 residues processed: 286 average time/residue: 0.5317 time to fit residues: 181.4507 Evaluate side-chains 284 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 243 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 722 THR Chi-restraints excluded: chain D residue 737 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 46 optimal weight: 0.0980 chunk 187 optimal weight: 0.9980 chunk 327 optimal weight: 3.9990 chunk 300 optimal weight: 4.9990 chunk 313 optimal weight: 0.5980 chunk 293 optimal weight: 3.9990 chunk 236 optimal weight: 0.7980 chunk 268 optimal weight: 3.9990 chunk 164 optimal weight: 20.0000 chunk 253 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 740 HIS C 740 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.214582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.151985 restraints weight = 27715.983| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.48 r_work: 0.3312 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 28100 Z= 0.111 Angle : 0.566 10.489 38176 Z= 0.291 Chirality : 0.045 0.184 4384 Planarity : 0.004 0.051 4988 Dihedral : 21.746 169.632 4540 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.49 % Favored : 96.39 % Rotamer: Outliers : 1.72 % Allowed : 11.95 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.14), residues: 3464 helix: 0.31 (0.15), residues: 1348 sheet: 0.24 (0.22), residues: 592 loop : -1.17 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 26 TYR 0.019 0.001 TYR C 256 PHE 0.011 0.001 PHE C 692 TRP 0.009 0.001 TRP D 763 HIS 0.006 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (28088) covalent geometry : angle 0.56617 / 0.29 (38176) hydrogen bonds : bond 0.03963 / 2.65 ( 1116) hydrogen bonds : angle 4.49894 / 3.16 ( 3084) metal coordination : bond 0.00354 / 0.21 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13018.25 seconds wall clock time: 221 minutes 30.55 seconds (13290.55 seconds total)