Starting phenix.real_space_refine on Wed Aug 27 01:46:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uh2_42244/08_2025/8uh2_42244.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uh2_42244/08_2025/8uh2_42244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uh2_42244/08_2025/8uh2_42244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uh2_42244/08_2025/8uh2_42244.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uh2_42244/08_2025/8uh2_42244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uh2_42244/08_2025/8uh2_42244.map" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24859 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 15831 2.51 5 N 4213 2.21 5 O 4738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24887 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 940 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 112} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "A" Number of atoms: 4961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 4961 Classifications: {'peptide': 640} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 602} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 6472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 6472 Classifications: {'peptide': 895} Incomplete info: {'truncation_to_alanine': 179} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 856} Chain breaks: 3 Unresolved non-hydrogen bonds: 699 Unresolved non-hydrogen angles: 872 Unresolved non-hydrogen dihedrals: 580 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASP:plan': 22, 'GLU:plan': 32, 'GLN:plan1': 22, 'ARG:plan': 10, 'HIS:plan': 3, 'PHE:plan': 9, 'ASN:plan1': 12, 'TRP:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 485 Chain: "G" Number of atoms: 4986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 4986 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 604} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 6528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 6528 Classifications: {'peptide': 898} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 858} Chain breaks: 2 Unresolved non-hydrogen bonds: 663 Unresolved non-hydrogen angles: 825 Unresolved non-hydrogen dihedrals: 553 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLU:plan': 30, 'ARG:plan': 9, 'GLN:plan1': 20, 'ASP:plan': 19, 'HIS:plan': 3, 'ASN:plan1': 11, 'TYR:plan': 6, 'PHE:plan': 7, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 452 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.35, per 1000 atoms: 0.26 Number of scatterers: 24887 At special positions: 0 Unit cell: (130.24, 176, 171.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4738 8.00 N 4213 7.00 C 15831 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 113 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 58 " - pdb=" SG CYS D 113 " distance=2.02 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS B 794 " distance=2.04 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS A 640 " distance=2.03 Simple disulfide: pdb=" SG CYS B 851 " - pdb=" SG CYS B1491 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1136 " distance=2.03 Simple disulfide: pdb=" SG CYS B1336 " - pdb=" SG CYS B1467 " distance=2.03 Simple disulfide: pdb=" SG CYS B1367 " - pdb=" SG CYS B1436 " distance=2.05 Simple disulfide: pdb=" SG CYS B1484 " - pdb=" SG CYS B1489 " distance=2.03 Simple disulfide: pdb=" SG CYS B1496 " - pdb=" SG CYS B1568 " distance=2.03 Simple disulfide: pdb=" SG CYS B1515 " - pdb=" SG CYS B1639 " distance=2.03 Simple disulfide: pdb=" SG CYS B1615 " - pdb=" SG CYS B1624 " distance=2.03 Simple disulfide: pdb=" SG CYS G 537 " - pdb=" SG CYS H 794 " distance=2.03 Simple disulfide: pdb=" SG CYS G 605 " - pdb=" SG CYS G 640 " distance=2.03 Simple disulfide: pdb=" SG CYS H 851 " - pdb=" SG CYS H1491 " distance=2.03 Simple disulfide: pdb=" SG CYS H1079 " - pdb=" SG CYS H1136 " distance=2.03 Simple disulfide: pdb=" SG CYS H1336 " - pdb=" SG CYS H1467 " distance=2.03 Simple disulfide: pdb=" SG CYS H1367 " - pdb=" SG CYS H1436 " distance=2.05 Simple disulfide: pdb=" SG CYS H1484 " - pdb=" SG CYS H1489 " distance=2.03 Simple disulfide: pdb=" SG CYS H1496 " - pdb=" SG CYS H1568 " distance=2.03 Simple disulfide: pdb=" SG CYS H1515 " - pdb=" SG CYS H1639 " distance=2.03 Simple disulfide: pdb=" SG CYS H1615 " - pdb=" SG CYS H1624 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 63 " " NAG B1701 " - " ASN B 917 " " NAG G 701 " - " ASN G 63 " " NAG H1701 " - " ASN H 917 " Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6240 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 49 sheets defined 25.1% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'C' and resid 2 through 14 removed outlier: 3.540A pdb=" N THR C 14 " --> pdb=" O LYS C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 38 Processing helix chain 'C' and resid 39 through 46 Processing helix chain 'C' and resid 55 through 79 removed outlier: 3.775A pdb=" N VAL C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 111 removed outlier: 4.007A pdb=" N ASP C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 38 through 47 removed outlier: 3.740A pdb=" N GLY D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 79 removed outlier: 3.795A pdb=" N VAL D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 110 removed outlier: 3.896A pdb=" N ASP D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP D 98 " --> pdb=" O ASP D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 263 through 266 removed outlier: 4.212A pdb=" N LEU A 266 " --> pdb=" O PRO A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 266' Processing helix chain 'A' and resid 281 through 289 removed outlier: 3.611A pdb=" N VAL A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.975A pdb=" N GLN A 414 " --> pdb=" O GLU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.709A pdb=" N GLU A 462 " --> pdb=" O ARG A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.928A pdb=" N PHE A 503 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 504 " --> pdb=" O THR A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 504' Processing helix chain 'A' and resid 578 through 584 Processing helix chain 'A' and resid 590 through 600 Processing helix chain 'A' and resid 612 through 621 Processing helix chain 'B' and resid 977 through 981 removed outlier: 4.367A pdb=" N HIS B 980 " --> pdb=" O ARG B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1010 Proline residue: B 998 - end of helix Processing helix chain 'B' and resid 1011 through 1016 removed outlier: 3.511A pdb=" N PHE B1015 " --> pdb=" O GLN B1011 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B1016 " --> pdb=" O TRP B1012 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1011 through 1016' Processing helix chain 'B' and resid 1018 through 1037 removed outlier: 4.034A pdb=" N GLY B1022 " --> pdb=" O GLU B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1053 through 1068 Processing helix chain 'B' and resid 1074 through 1089 removed outlier: 3.544A pdb=" N LEU B1078 " --> pdb=" O ASP B1074 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B1088 " --> pdb=" O TRP B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1108 through 1113 removed outlier: 3.881A pdb=" N LEU B1111 " --> pdb=" O ILE B1108 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B1112 " --> pdb=" O GLY B1109 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1132 Processing helix chain 'B' and resid 1142 through 1157 removed outlier: 3.694A pdb=" N ASN B1157 " --> pdb=" O PHE B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1178 removed outlier: 3.885A pdb=" N MET B1177 " --> pdb=" O ALA B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1182 through 1191 removed outlier: 4.103A pdb=" N ASN B1186 " --> pdb=" O GLY B1182 " (cutoff:3.500A) Processing helix chain 'B' and resid 1203 through 1222 removed outlier: 3.938A pdb=" N ASN B1207 " --> pdb=" O LYS B1203 " (cutoff:3.500A) Processing helix chain 'B' and resid 1226 through 1238 Processing helix chain 'B' and resid 1246 through 1261 Processing helix chain 'B' and resid 1292 through 1294 No H-bonds generated for 'chain 'B' and resid 1292 through 1294' Processing helix chain 'B' and resid 1392 through 1402 removed outlier: 3.658A pdb=" N LEU B1396 " --> pdb=" O ASP B1392 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS B1397 " --> pdb=" O THR B1393 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN B1398 " --> pdb=" O ASP B1394 " (cutoff:3.500A) Processing helix chain 'B' and resid 1408 through 1415 removed outlier: 3.648A pdb=" N LYS B1414 " --> pdb=" O TYR B1410 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B1415 " --> pdb=" O GLU B1411 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1419 removed outlier: 3.628A pdb=" N ARG B1419 " --> pdb=" O PHE B1416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1416 through 1419' Processing helix chain 'B' and resid 1506 through 1514 removed outlier: 4.079A pdb=" N ARG B1510 " --> pdb=" O THR B1506 " (cutoff:3.500A) Processing helix chain 'B' and resid 1567 through 1572 removed outlier: 3.809A pdb=" N ALA B1571 " --> pdb=" O LYS B1567 " (cutoff:3.500A) Processing helix chain 'B' and resid 1585 through 1587 No H-bonds generated for 'chain 'B' and resid 1585 through 1587' Processing helix chain 'B' and resid 1613 through 1616 Processing helix chain 'B' and resid 1617 through 1637 removed outlier: 4.034A pdb=" N LYS B1622 " --> pdb=" O GLU B1618 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN B1623 " --> pdb=" O GLU B1619 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B1632 " --> pdb=" O GLY B1628 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B1635 " --> pdb=" O THR B1631 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 71 through 76 Processing helix chain 'G' and resid 263 through 266 removed outlier: 4.001A pdb=" N LEU G 266 " --> pdb=" O PRO G 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 263 through 266' Processing helix chain 'G' and resid 281 through 289 removed outlier: 4.073A pdb=" N VAL G 289 " --> pdb=" O LEU G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 298 Processing helix chain 'G' and resid 461 through 465 removed outlier: 3.550A pdb=" N LYS G 464 " --> pdb=" O HIS G 461 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE G 465 " --> pdb=" O GLU G 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 461 through 465' Processing helix chain 'G' and resid 500 through 504 removed outlier: 3.727A pdb=" N PHE G 503 " --> pdb=" O THR G 500 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE G 504 " --> pdb=" O THR G 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 500 through 504' Processing helix chain 'G' and resid 578 through 584 Processing helix chain 'G' and resid 590 through 601 removed outlier: 3.570A pdb=" N ALA G 601 " --> pdb=" O VAL G 597 " (cutoff:3.500A) Processing helix chain 'G' and resid 612 through 621 Processing helix chain 'H' and resid 988 through 1010 Proline residue: H 998 - end of helix removed outlier: 3.694A pdb=" N ILE H1001 " --> pdb=" O THR H 997 " (cutoff:3.500A) Processing helix chain 'H' and resid 1011 through 1016 removed outlier: 4.912A pdb=" N GLY H1016 " --> pdb=" O GLU H1013 " (cutoff:3.500A) Processing helix chain 'H' and resid 1017 through 1037 removed outlier: 4.142A pdb=" N GLN H1021 " --> pdb=" O LEU H1017 " (cutoff:3.500A) Processing helix chain 'H' and resid 1053 through 1068 Processing helix chain 'H' and resid 1074 through 1088 Processing helix chain 'H' and resid 1104 through 1113 removed outlier: 4.243A pdb=" N MET H1107 " --> pdb=" O HIS H1104 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE H1108 " --> pdb=" O GLN H1105 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY H1109 " --> pdb=" O GLU H1106 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY H1110 " --> pdb=" O MET H1107 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU H1111 " --> pdb=" O ILE H1108 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG H1112 " --> pdb=" O GLY H1109 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN H1113 " --> pdb=" O GLY H1110 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1104 through 1113' Processing helix chain 'H' and resid 1116 through 1132 removed outlier: 3.566A pdb=" N ALA H1120 " --> pdb=" O GLU H1116 " (cutoff:3.500A) Processing helix chain 'H' and resid 1142 through 1157 Processing helix chain 'H' and resid 1163 through 1177 Processing helix chain 'H' and resid 1182 through 1192 removed outlier: 3.693A pdb=" N ASN H1186 " --> pdb=" O GLY H1182 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA H1192 " --> pdb=" O PHE H1188 " (cutoff:3.500A) Processing helix chain 'H' and resid 1203 through 1221 removed outlier: 3.672A pdb=" N ASN H1207 " --> pdb=" O LYS H1203 " (cutoff:3.500A) Processing helix chain 'H' and resid 1226 through 1238 removed outlier: 3.924A pdb=" N VAL H1230 " --> pdb=" O PHE H1226 " (cutoff:3.500A) Processing helix chain 'H' and resid 1247 through 1263 removed outlier: 3.566A pdb=" N ASP H1263 " --> pdb=" O GLN H1259 " (cutoff:3.500A) Processing helix chain 'H' and resid 1392 through 1401 removed outlier: 3.766A pdb=" N ASN H1401 " --> pdb=" O LYS H1397 " (cutoff:3.500A) Processing helix chain 'H' and resid 1408 through 1413 Processing helix chain 'H' and resid 1506 through 1514 removed outlier: 4.020A pdb=" N ARG H1510 " --> pdb=" O THR H1506 " (cutoff:3.500A) Processing helix chain 'H' and resid 1566 through 1572 removed outlier: 3.908A pdb=" N GLU H1570 " --> pdb=" O ILE H1566 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA H1571 " --> pdb=" O LYS H1567 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU H1572 " --> pdb=" O CYS H1568 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1566 through 1572' Processing helix chain 'H' and resid 1617 through 1638 removed outlier: 3.562A pdb=" N VAL H1636 " --> pdb=" O GLU H1632 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.680A pdb=" N LYS A 82 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE A 83 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 31 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 112 removed outlier: 3.643A pdb=" N TYR A 125 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.540A pdb=" N LYS A 183 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 141 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SER A 157 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A 143 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN A 155 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 145 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 210 through 216 removed outlier: 3.682A pdb=" N THR A 232 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 222 removed outlier: 7.507A pdb=" N MET A 316 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU A 310 " --> pdb=" O MET A 316 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLN A 318 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL A 308 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLU A 320 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ALA A 306 " --> pdb=" O GLU A 320 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER A 322 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 304 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 221 through 222 removed outlier: 7.507A pdb=" N MET A 316 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU A 310 " --> pdb=" O MET A 316 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLN A 318 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL A 308 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLU A 320 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ALA A 306 " --> pdb=" O GLU A 320 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER A 322 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 304 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 332 through 334 removed outlier: 3.815A pdb=" N ILE A 389 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 352 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AB1, first strand: chain 'A' and resid 433 through 437 removed outlier: 4.028A pdb=" N ARG A 456 " --> pdb=" O TYR A 433 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 451 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 495 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 477 through 482 removed outlier: 6.803A pdb=" N ILE A 472 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA A 481 " --> pdb=" O TYR A 470 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR A 470 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET A 473 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 525 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 515 " --> pdb=" O GLU A 523 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 523 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 517 " --> pdb=" O GLN A 521 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 543 through 545 Processing sheet with id=AB4, first strand: chain 'B' and resid 748 through 755 removed outlier: 7.139A pdb=" N SER B 748 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP A 577 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU B 750 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA A 575 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN B 752 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 570 " --> pdb=" O MET B 787 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 748 through 755 removed outlier: 7.139A pdb=" N SER B 748 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP A 577 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU B 750 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA A 575 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN B 752 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 570 " --> pdb=" O MET B 787 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 807 through 812 removed outlier: 3.798A pdb=" N VAL B 828 " --> pdb=" O ASP B 810 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG B 826 " --> pdb=" O ARG B 812 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 816 through 818 removed outlier: 3.745A pdb=" N VAL B 910 " --> pdb=" O VAL B 817 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP B 901 " --> pdb=" O ALA B 892 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 884 " --> pdb=" O VAL B 909 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 841 through 844 removed outlier: 4.618A pdb=" N HIS B 860 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 914 through 916 removed outlier: 4.007A pdb=" N ALA B 921 " --> pdb=" O VAL B1322 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR B1324 " --> pdb=" O THR B 919 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N THR B 919 " --> pdb=" O THR B1324 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 914 through 916 Processing sheet with id=AC2, first strand: chain 'B' and resid 936 through 940 removed outlier: 3.635A pdb=" N ILE B1285 " --> pdb=" O LEU B1276 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1342 through 1347 removed outlier: 3.683A pdb=" N LEU B1437 " --> pdb=" O ILE B1366 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1405 through 1406 removed outlier: 3.604A pdb=" N VAL B1457 " --> pdb=" O CYS B1467 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1482 through 1485 removed outlier: 3.566A pdb=" N ARG B1485 " --> pdb=" O LEU B1488 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1546 through 1548 removed outlier: 6.496A pdb=" N VAL B1522 " --> pdb=" O ILE B1547 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU B1527 " --> pdb=" O ALA B1542 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA B1542 " --> pdb=" O LEU B1527 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B1529 " --> pdb=" O ILE B1540 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP B1590 " --> pdb=" O SER B1597 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1546 through 1548 removed outlier: 6.496A pdb=" N VAL B1522 " --> pdb=" O ILE B1547 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET B1582 " --> pdb=" O TYR B1523 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B1525 " --> pdb=" O TYR B1580 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS B1579 " --> pdb=" O TRP B1609 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP B1583 " --> pdb=" O TRP B1605 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP B1605 " --> pdb=" O TRP B1583 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 61 through 66 removed outlier: 4.280A pdb=" N PHE G 66 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU G 18 " --> pdb=" O PHE G 66 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N THR G 19 " --> pdb=" O PRO G 9 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.530A pdb=" N LYS G 82 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE G 83 " --> pdb=" O PHE G 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 107 through 112 removed outlier: 3.569A pdb=" N PHE G 128 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR G 125 " --> pdb=" O LEU G 169 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU G 167 " --> pdb=" O ILE G 127 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 116 through 117 removed outlier: 6.712A pdb=" N VAL G 141 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER G 157 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL G 143 " --> pdb=" O GLN G 155 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLN G 155 " --> pdb=" O VAL G 143 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE G 145 " --> pdb=" O VAL G 153 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 210 through 216 removed outlier: 3.634A pdb=" N THR G 232 " --> pdb=" O GLU G 215 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 221 through 222 removed outlier: 5.508A pdb=" N TYR G 221 " --> pdb=" O VAL G 327 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N MET G 316 " --> pdb=" O LEU G 310 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU G 310 " --> pdb=" O MET G 316 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN G 318 " --> pdb=" O VAL G 308 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL G 308 " --> pdb=" O GLN G 318 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLU G 320 " --> pdb=" O ALA G 306 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA G 306 " --> pdb=" O GLU G 320 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N SER G 322 " --> pdb=" O VAL G 304 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL G 304 " --> pdb=" O SER G 322 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 221 through 222 removed outlier: 5.508A pdb=" N TYR G 221 " --> pdb=" O VAL G 327 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N MET G 316 " --> pdb=" O LEU G 310 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU G 310 " --> pdb=" O MET G 316 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN G 318 " --> pdb=" O VAL G 308 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL G 308 " --> pdb=" O GLN G 318 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLU G 320 " --> pdb=" O ALA G 306 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA G 306 " --> pdb=" O GLU G 320 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N SER G 322 " --> pdb=" O VAL G 304 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL G 304 " --> pdb=" O SER G 322 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY G 245 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA G 247 " --> pdb=" O ILE G 269 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 332 through 334 removed outlier: 3.511A pdb=" N PHE G 348 " --> pdb=" O ILE G 389 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL G 352 " --> pdb=" O ALA G 385 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 341 through 342 Processing sheet with id=AD8, first strand: chain 'G' and resid 433 through 438 removed outlier: 3.635A pdb=" N TYR G 433 " --> pdb=" O ARG G 456 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL G 451 " --> pdb=" O LEU G 495 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 469 through 471 removed outlier: 3.750A pdb=" N VAL G 525 " --> pdb=" O TYR G 513 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU G 515 " --> pdb=" O GLU G 523 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU G 523 " --> pdb=" O LEU G 515 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 543 through 545 Processing sheet with id=AE2, first strand: chain 'H' and resid 748 through 755 removed outlier: 4.944A pdb=" N LEU H 750 " --> pdb=" O ALA G 575 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA G 575 " --> pdb=" O LEU H 750 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN H 752 " --> pdb=" O LEU G 573 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG G 570 " --> pdb=" O MET H 787 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 748 through 755 removed outlier: 4.944A pdb=" N LEU H 750 " --> pdb=" O ALA G 575 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA G 575 " --> pdb=" O LEU H 750 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN H 752 " --> pdb=" O LEU G 573 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG G 570 " --> pdb=" O MET H 787 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 809 through 812 removed outlier: 3.905A pdb=" N ARG H 826 " --> pdb=" O ARG H 812 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU H 872 " --> pdb=" O LEU H 829 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 816 through 818 removed outlier: 3.727A pdb=" N VAL H 910 " --> pdb=" O VAL H 817 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY H 884 " --> pdb=" O VAL H 909 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N HIS H 860 " --> pdb=" O LEU H 844 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 914 through 916 removed outlier: 3.957A pdb=" N ALA H 921 " --> pdb=" O VAL H1322 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR H1324 " --> pdb=" O THR H 919 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR H 919 " --> pdb=" O THR H1324 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 914 through 916 Processing sheet with id=AE8, first strand: chain 'H' and resid 935 through 940 removed outlier: 3.576A pdb=" N PHE H1308 " --> pdb=" O ILE H 940 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 1038 through 1039 removed outlier: 3.717A pdb=" N ALA H1043 " --> pdb=" O GLN H1039 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 1340 through 1347 removed outlier: 3.536A pdb=" N LEU H1437 " --> pdb=" O ILE H1366 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 1405 through 1406 removed outlier: 3.516A pdb=" N TYR H1458 " --> pdb=" O ILE H1380 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS H1456 " --> pdb=" O ASP H1382 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 1482 through 1484 Processing sheet with id=AF4, first strand: chain 'H' and resid 1589 through 1590 removed outlier: 7.213A pdb=" N PHE H1536 " --> pdb=" O LEU H1532 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU H1532 " --> pdb=" O PHE H1536 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU H1538 " --> pdb=" O VAL H1530 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL H1530 " --> pdb=" O GLU H1538 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILE H1540 " --> pdb=" O VAL H1528 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA H1542 " --> pdb=" O ARG H1526 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG H1526 " --> pdb=" O ALA H1542 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS H1524 " --> pdb=" O GLU H1544 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR H1546 " --> pdb=" O VAL H1522 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL H1522 " --> pdb=" O THR H1546 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR H1521 " --> pdb=" O GLY H1584 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N HIS H1579 " --> pdb=" O TRP H1609 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 2991 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.66 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8198 1.34 - 1.47: 5734 1.47 - 1.59: 11270 1.59 - 1.71: 0 1.71 - 1.84: 161 Bond restraints: 25363 Sorted by residual: bond pdb=" N HIS B 897 " pdb=" CA HIS B 897 " ideal model delta sigma weight residual 1.452 1.482 -0.029 1.22e-02 6.72e+03 5.73e+00 bond pdb=" N HIS H 896 " pdb=" CA HIS H 896 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.00e+00 bond pdb=" N HIS B 896 " pdb=" CA HIS B 896 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.86e+00 bond pdb=" N HIS H 897 " pdb=" CA HIS H 897 " ideal model delta sigma weight residual 1.452 1.479 -0.027 1.22e-02 6.72e+03 4.83e+00 bond pdb=" CG HIS B 897 " pdb=" ND1 HIS B 897 " ideal model delta sigma weight residual 1.378 1.358 0.020 1.10e-02 8.26e+03 3.18e+00 ... (remaining 25358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 34010 2.18 - 4.37: 470 4.37 - 6.55: 46 6.55 - 8.73: 4 8.73 - 10.92: 2 Bond angle restraints: 34532 Sorted by residual: angle pdb=" C HIS H 896 " pdb=" CA HIS H 896 " pdb=" CB HIS H 896 " ideal model delta sigma weight residual 110.42 121.34 -10.92 1.99e+00 2.53e-01 3.01e+01 angle pdb=" C HIS B 896 " pdb=" CA HIS B 896 " pdb=" CB HIS B 896 " ideal model delta sigma weight residual 110.42 120.98 -10.56 1.99e+00 2.53e-01 2.81e+01 angle pdb=" C HIS B 896 " pdb=" N HIS B 897 " pdb=" CA HIS B 897 " ideal model delta sigma weight residual 122.64 114.14 8.50 1.77e+00 3.19e-01 2.31e+01 angle pdb=" CA HIS H 896 " pdb=" CB HIS H 896 " pdb=" CG HIS H 896 " ideal model delta sigma weight residual 113.80 109.44 4.36 1.00e+00 1.00e+00 1.90e+01 angle pdb=" C ASP G 550 " pdb=" CA ASP G 550 " pdb=" CB ASP G 550 " ideal model delta sigma weight residual 115.79 110.72 5.07 1.19e+00 7.06e-01 1.81e+01 ... (remaining 34527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 14422 21.89 - 43.79: 882 43.79 - 65.68: 99 65.68 - 87.58: 37 87.58 - 109.47: 13 Dihedral angle restraints: 15453 sinusoidal: 5802 harmonic: 9651 Sorted by residual: dihedral pdb=" CB CYS A 537 " pdb=" SG CYS A 537 " pdb=" SG CYS B 794 " pdb=" CB CYS B 794 " ideal model delta sinusoidal sigma weight residual 93.00 160.51 -67.51 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CB CYS D 58 " pdb=" SG CYS D 58 " pdb=" SG CYS D 113 " pdb=" CB CYS D 113 " ideal model delta sinusoidal sigma weight residual -86.00 -144.94 58.94 1 1.00e+01 1.00e-02 4.65e+01 dihedral pdb=" C HIS H 896 " pdb=" N HIS H 896 " pdb=" CA HIS H 896 " pdb=" CB HIS H 896 " ideal model delta harmonic sigma weight residual -122.60 -139.19 16.59 0 2.50e+00 1.60e-01 4.41e+01 ... (remaining 15450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 3979 0.110 - 0.221: 98 0.221 - 0.331: 0 0.331 - 0.442: 0 0.442 - 0.552: 2 Chirality restraints: 4079 Sorted by residual: chirality pdb=" CA HIS H 896 " pdb=" N HIS H 896 " pdb=" C HIS H 896 " pdb=" CB HIS H 896 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" CA HIS B 896 " pdb=" N HIS B 896 " pdb=" C HIS B 896 " pdb=" CB HIS B 896 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 63 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 4076 not shown) Planarity restraints: 4447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR H 895 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.44e+00 pdb=" C TYR H 895 " -0.050 2.00e-02 2.50e+03 pdb=" O TYR H 895 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS H 896 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 895 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C TYR B 895 " 0.044 2.00e-02 2.50e+03 pdb=" O TYR B 895 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS B 896 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 897 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C HIS H 897 " -0.042 2.00e-02 2.50e+03 pdb=" O HIS H 897 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE H 898 " 0.014 2.00e-02 2.50e+03 ... (remaining 4444 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 397 2.67 - 3.23: 23578 3.23 - 3.79: 36414 3.79 - 4.34: 46523 4.34 - 4.90: 79477 Nonbonded interactions: 186389 Sorted by model distance: nonbonded pdb=" NH2 ARG H 826 " pdb=" OG SER H1384 " model vdw 2.117 3.120 nonbonded pdb=" O ASN B 762 " pdb=" ND2 ASN B 762 " model vdw 2.143 3.120 nonbonded pdb=" NH2 ARG B 826 " pdb=" OG SER B1384 " model vdw 2.157 3.120 nonbonded pdb=" OG SER B1432 " pdb=" OE1 GLU B1433 " model vdw 2.174 3.040 nonbonded pdb=" ND2 ASN B 992 " pdb=" OE1 GLN B1034 " model vdw 2.178 3.120 ... (remaining 186384 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 84 or (resid 85 and (name N or name CA or name C \ or name O or name CB )) or resid 86 through 547 or (resid 548 through 549 and ( \ name N or name CA or name C or name O or name CB )) or resid 550 through 701)) selection = (chain 'G' and (resid 1 through 43 or resid 45 through 71 or resid 73 through 14 \ 7 or (resid 148 and (name N or name CA or name C or name O or name CB )) or resi \ d 149 through 243 or (resid 244 and (name N or name CA or name C or name O or na \ me CB )) or resid 245 through 256 or (resid 257 and (name N or name CA or name C \ or name O or name CB )) or resid 258 through 599 or (resid 600 through 601 and \ (name N or name CA or name C or name O or name CB )) or resid 602 through 641 or \ (resid 642 and (name N or name CA or name C or name O or name CB )) or resid 70 \ 1)) } ncs_group { reference = (chain 'B' and (resid 731 through 923 or (resid 924 and (name N or name CA or na \ me C or name O or name CB )) or resid 925 through 927 or (resid 928 through 929 \ and (name N or name CA or name C or name O or name CB )) or resid 935 or (resid \ 936 through 937 and (name N or name CA or name C or name O or name CB )) or resi \ d 938 through 943 or (resid 944 through 945 and (name N or name CA or name C or \ name O or name CB )) or resid 946 through 947 or (resid 948 and (name N or name \ CA or name C or name O or name CB )) or resid 949 through 978 or (resid 979 thro \ ugh 980 and (name N or name CA or name C or name O or name CB )) or resid 981 or \ (resid 983 through 984 and (name N or name CA or name C or name O or name CB )) \ or resid 985 or (resid 986 and (name N or name CA or name C or name O or name C \ B )) or resid 987 or (resid 988 and (name N or name CA or name C or name O or na \ me CB )) or resid 989 or (resid 990 through 994 and (name N or name CA or name C \ or name O or name CB )) or resid 995 or (resid 996 through 997 and (name N or n \ ame CA or name C or name O or name CB )) or resid 998 or (resid 999 through 1002 \ and (name N or name CA or name C or name O or name CB )) or resid 1003 through \ 1013 or (resid 1014 and (name N or name CA or name C or name O or name CB )) or \ resid 1015 through 1017 or (resid 1018 through 1019 and (name N or name CA or na \ me C or name O or name CB )) or resid 1020 through 1027 or (resid 1028 through 1 \ 029 and (name N or name CA or name C or name O or name CB )) or resid 1030 or (r \ esid 1031 through 1039 and (name N or name CA or name C or name O or name CB )) \ or resid 1040 through 1041 or (resid 1042 through 1049 and (name N or name CA or \ name C or name O or name CB )) or resid 1050 through 1052 or (resid 1053 throug \ h 1058 and (name N or name CA or name C or name O or name CB )) or resid 1059 or \ (resid 1060 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 061 through 1062 or (resid 1063 through 1064 and (name N or name CA or name C or \ name O or name CB )) or resid 1065 through 1070 or (resid 1071 through 1076 and \ (name N or name CA or name C or name O or name CB )) or resid 1077 through 1082 \ or (resid 1083 through 1084 and (name N or name CA or name C or name O or name \ CB )) or resid 1085 through 1088 or (resid 1089 through 1091 and (name N or name \ CA or name C or name O or name CB )) or resid 1092 through 1094 or (resid 1095 \ and (name N or name CA or name C or name O or name CB )) or resid 1096 through 1 \ 097 or (resid 1098 through 1100 and (name N or name CA or name C or name O or na \ me CB )) or resid 1101 through 1103 or (resid 1104 through 1106 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1107 through 1112 or (resid 11 \ 13 through 1121 and (name N or name CA or name C or name O or name CB )) or resi \ d 1122 through 1130 or (resid 1131 through 1135 and (name N or name CA or name C \ or name O or name CB )) or resid 1136 through 1157 or (resid 1158 through 1160 \ and (name N or name CA or name C or name O or name CB )) or resid 1161 through 1 \ 164 or (resid 1165 and (name N or name CA or name C or name O or name CB )) or r \ esid 1166 through 1176 or (resid 1177 and (name N or name CA or name C or name O \ or name CB )) or resid 1178 through 1198 or (resid 1199 through 1200 and (name \ N or name CA or name C or name O or name CB )) or resid 1201 through 1204 or (re \ sid 1205 through 1207 and (name N or name CA or name C or name O or name CB )) o \ r resid 1208 or (resid 1209 through 1210 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1211 through 1237 or (resid 1238 and (name N or name \ CA or name C or name O or name CB )) or resid 1239 through 1260 or (resid 1261 t \ hrough 1264 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 65 through 1270 or (resid 1271 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1272 through 1289 or (resid 1290 through 1292 and (name N or na \ me CA or name C or name O or name CB )) or resid 1293 through 1328 or (resid 132 \ 9 through 1333 and (name N or name CA or name C or name O or name CB )) or resid \ 1334 through 1554 or (resid 1555 through 1556 and (name N or name CA or name C \ or name O or name CB )) or resid 1557 through 1625 or (resid 1626 and (name N or \ name CA or name C or name O or name CB )) or resid 1627 through 1701)) selection = (chain 'H' and (resid 731 through 929 or resid 935 through 960 or (resid 961 and \ (name N or name CA or name C or name O or name CB )) or resid 962 through 968 o \ r (resid 969 through 972 and (name N or name CA or name C or name O or name CB ) \ ) or resid 973 through 981 or resid 983 through 999 or (resid 1000 through 1002 \ and (name N or name CA or name C or name O or name CB )) or resid 1003 or (resid \ 1004 and (name N or name CA or name C or name O or name CB )) or resid 1005 thr \ ough 1061 or (resid 1062 through 1064 and (name N or name CA or name C or name O \ or name CB )) or resid 1065 through 1072 or (resid 1073 through 1076 and (name \ N or name CA or name C or name O or name CB )) or resid 1077 through 1083 or (re \ sid 1084 and (name N or name CA or name C or name O or name CB )) or resid 1085 \ through 1110 or (resid 1111 through 1121 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1122 through 1123 or (resid 1124 and (name N or name \ CA or name C or name O or name CB )) or resid 1125 or (resid 1126 through 1127 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1128 or (resid \ 1129 through 1135 and (name N or name CA or name C or name O or name CB )) or re \ sid 1136 through 1138 or (resid 1139 and (name N or name CA or name C or name O \ or name CB )) or resid 1140 through 1141 or (resid 1142 through 1143 and (name N \ or name CA or name C or name O or name CB )) or resid 1144 through 1147 or (res \ id 1148 through 1150 and (name N or name CA or name C or name O or name CB )) or \ resid 1151 or (resid 1152 through 1154 and (name N or name CA or name C or name \ O or name CB )) or resid 1155 through 1156 or (resid 1157 through 1160 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1161 through 1163 or ( \ resid 1164 through 1165 and (name N or name CA or name C or name O or name CB )) \ or resid 1166 through 1180 or (resid 1181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1182 through 1185 or (resid 1186 through 1187 and ( \ name N or name CA or name C or name O or name CB )) or resid 1188 through 1189 o \ r (resid 1190 through 1192 and (name N or name CA or name C or name O or name CB \ )) or resid 1193 through 1254 or (resid 1255 through 1258 and (name N or name C \ A or name C or name O or name CB )) or resid 1259 through 1261 or (resid 1262 th \ rough 1264 and (name N or name CA or name C or name O or name CB )) or resid 126 \ 5 through 1266 or (resid 1267 and (name N or name CA or name C or name O or name \ CB )) or resid 1268 through 1272 or (resid 1273 and (name N or name CA or name \ C or name O or name CB )) or resid 1274 through 1285 or (resid 1286 and (name N \ or name CA or name C or name O or name CB )) or resid 1287 through 1294 or (resi \ d 1295 through 1296 and (name N or name CA or name C or name O or name CB )) or \ resid 1297 through 1312 or (resid 1313 and (name N or name CA or name C or name \ O or name CB )) or (resid 1314 through 1317 and (name N or name CA or name C or \ name O or name CB )) or resid 1318 through 1348 or resid 1360 through 1391 or (r \ esid 1392 and (name N or name CA or name C or name O or name CB )) or resid 1393 \ through 1463 or (resid 1464 and (name N or name CA or name C or name O or name \ CB )) or resid 1465 through 1485 or (resid 1486 and (name N or name CA or name C \ or name O or name CB )) or resid 1487 through 1493 or (resid 1494 through 1495 \ and (name N or name CA or name C or name O or name CB )) or resid 1496 or (resid \ 1497 and (name N or name CA or name C or name O or name CB )) or resid 1498 or \ (resid 1499 through 1504 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1505 through 1506 or (resid 1507 through 1514 and (name N or name CA \ or name C or name O or name CB )) or resid 1515 through 1518 or (resid 1519 thro \ ugh 1520 and (name N or name CA or name C or name O or name CB )) or resid 1521 \ through 1525 or (resid 1526 and (name N or name CA or name C or name O or name C \ B )) or resid 1527 or (resid 1528 through 1529 and (name N or name CA or name C \ or name O or name CB )) or resid 1530 or (resid 1531 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1532 through 1533 or (resid 1534 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1535 through 1539 or ( \ resid 1540 and (name N or name CA or name C or name O or name CB )) or resid 154 \ 1 through 1543 or (resid 1544 through 1545 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1546 or (resid 1547 through 1549 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1550 through 1553 or (resid 1554 \ through 1556 and (name N or name CA or name C or name O or name CB )) or resid \ 1557 through 1558 or (resid 1559 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1560 through 1568 or (resid 1569 through 1571 and (name N or \ name CA or name C or name O or name CB )) or resid 1572 through 1574 or (resid 1 \ 575 through 1577 and (name N or name CA or name C or name O or name CB )) or res \ id 1578 or (resid 1579 and (name N or name CA or name C or name O or name CB )) \ or resid 1580 through 1585 or (resid 1586 through 1587 and (name N or name CA or \ name C or name O or name CB )) or resid 1588 or (resid 1589 and (name N or name \ CA or name C or name O or name CB )) or resid 1590 through 1592 or (resid 1593 \ and (name N or name CA or name C or name O or name CB )) or resid 1594 or (resid \ 1595 and (name N or name CA or name C or name O or name CB )) or resid 1596 thr \ ough 1601 or (resid 1602 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1603 through 1604 or (resid 1605 and (name N or name CA or name C or \ name O or name CB )) or resid 1606 or (resid 1607 and (name N or name CA or name \ C or name O or name CB )) or resid 1608 or (resid 1609 and (name N or name CA o \ r name C or name O or name CB )) or resid 1610 or (resid 1611 through 1614 and ( \ name N or name CA or name C or name O or name CB )) or resid 1615 through 1620 o \ r (resid 1621 through 1623 and (name N or name CA or name C or name O or name CB \ )) or resid 1624 through 1634 or (resid 1635 and (name N or name CA or name C o \ r name O or name CB )) or resid 1636 through 1640 or (resid 1641 and (name N or \ name CA or name C or name O or name CB )) or resid 1701)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 1 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 116)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.240 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 25391 Z= 0.236 Angle : 0.629 10.918 34592 Z= 0.332 Chirality : 0.047 0.552 4079 Planarity : 0.004 0.057 4443 Dihedral : 14.362 109.472 9141 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.42 % Favored : 95.52 % Rotamer: Outliers : 0.12 % Allowed : 0.27 % Favored : 99.61 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.82 % 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 aren not related in a simple way. whole: 0.16 (0.15), residues: 3281 helix: 1.51 (0.20), residues: 722 sheet: 0.10 (0.17), residues: 1027 loop : -0.49 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 364 TYR 0.028 0.002 TYR C 67 PHE 0.029 0.002 PHE C 12 TRP 0.011 0.001 TRP H1590 HIS 0.009 0.001 HIS H 896 Details of bonding type rmsd covalent geometry : bond 0.00563 (25363) covalent geometry : angle 0.62490 (34532) SS BOND : bond 0.00538 ( 24) SS BOND : angle 1.76739 ( 48) hydrogen bonds : bond 0.22047 ( 1031) hydrogen bonds : angle 8.17443 ( 2991) link_NAG-ASN : bond 0.00160 ( 4) link_NAG-ASN : angle 1.88172 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 306 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: C 84 HIS cc_start: 0.6023 (m-70) cc_final: 0.5363 (m170) REVERT: C 101 THR cc_start: 0.7499 (m) cc_final: 0.7283 (m) REVERT: D 101 THR cc_start: 0.7426 (m) cc_final: 0.7149 (m) REVERT: A 201 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6769 (mt-10) REVERT: A 527 ASP cc_start: 0.8160 (t0) cc_final: 0.7950 (t0) REVERT: B 1213 TYR cc_start: 0.7823 (m-80) cc_final: 0.7461 (m-80) REVERT: B 1410 TYR cc_start: 0.6924 (t80) cc_final: 0.6395 (t80) REVERT: G 142 MET cc_start: 0.7340 (mmt) cc_final: 0.7107 (mmt) REVERT: G 175 GLU cc_start: 0.7443 (tp30) cc_final: 0.7206 (tp30) REVERT: G 376 GLN cc_start: 0.7674 (pp30) cc_final: 0.7213 (pp30) REVERT: H 1270 LEU cc_start: 0.7297 (pt) cc_final: 0.6573 (tp) REVERT: H 1481 ASN cc_start: 0.7429 (t0) cc_final: 0.6975 (t0) outliers start: 3 outliers final: 2 residues processed: 309 average time/residue: 0.1474 time to fit residues: 76.1330 Evaluate side-chains 250 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 248 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 897 HIS Chi-restraints excluded: chain H residue 897 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 HIS A 60 HIS ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 HIS A 334 HIS B 762 ASN B 980 HIS B1021 GLN B1090 GLN ** B1248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.192374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.154331 restraints weight = 34388.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.151063 restraints weight = 59778.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.153677 restraints weight = 50189.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.153498 restraints weight = 32173.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154468 restraints weight = 29920.139| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25391 Z= 0.137 Angle : 0.570 7.681 34592 Z= 0.301 Chirality : 0.045 0.180 4079 Planarity : 0.004 0.053 4443 Dihedral : 6.285 85.224 3621 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.04 % Rotamer: Outliers : 0.62 % Allowed : 8.92 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 aren not related in a simple way. whole: 0.30 (0.15), residues: 3281 helix: 1.57 (0.20), residues: 727 sheet: 0.30 (0.16), residues: 1067 loop : -0.50 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 923 TYR 0.026 0.001 TYR D 74 PHE 0.015 0.001 PHE A 507 TRP 0.021 0.001 TRP H1609 HIS 0.006 0.001 HIS G 311 Details of bonding type rmsd covalent geometry : bond 0.00315 (25363) covalent geometry : angle 0.56660 (34532) SS BOND : bond 0.00651 ( 24) SS BOND : angle 1.49852 ( 48) hydrogen bonds : bond 0.04091 ( 1031) hydrogen bonds : angle 5.79706 ( 2991) link_NAG-ASN : bond 0.00264 ( 4) link_NAG-ASN : angle 1.90022 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 288 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: C 74 TYR cc_start: 0.7729 (t80) cc_final: 0.7483 (t80) REVERT: A 201 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7121 (mt-10) REVERT: A 311 HIS cc_start: 0.6910 (m170) cc_final: 0.6674 (m170) REVERT: B 996 MET cc_start: 0.7403 (mtm) cc_final: 0.7150 (mtp) REVERT: B 1338 LYS cc_start: 0.7405 (ptpt) cc_final: 0.7196 (pptt) REVERT: G 523 GLU cc_start: 0.8158 (pp20) cc_final: 0.7671 (pp20) REVERT: H 1270 LEU cc_start: 0.6715 (pt) cc_final: 0.6219 (tp) REVERT: H 1385 MET cc_start: 0.8495 (tmm) cc_final: 0.8059 (tmm) outliers start: 16 outliers final: 9 residues processed: 296 average time/residue: 0.1610 time to fit residues: 78.7516 Evaluate side-chains 263 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 254 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain B residue 1021 GLN Chi-restraints excluded: chain B residue 1297 LEU Chi-restraints excluded: chain H residue 1339 PHE Chi-restraints excluded: chain H residue 1364 LEU Chi-restraints excluded: chain H residue 1486 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 122 optimal weight: 30.0000 chunk 21 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 233 optimal weight: 0.8980 chunk 272 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN B 980 HIS ** B 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1090 GLN H 846 HIS ** H 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.189428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.151259 restraints weight = 34516.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.146845 restraints weight = 61769.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.149080 restraints weight = 51957.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.150081 restraints weight = 30679.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.150699 restraints weight = 27464.007| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25391 Z= 0.150 Angle : 0.551 8.796 34592 Z= 0.288 Chirality : 0.044 0.205 4079 Planarity : 0.004 0.046 4443 Dihedral : 5.758 68.223 3617 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 1.05 % Allowed : 12.66 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 aren not related in a simple way. whole: 0.25 (0.15), residues: 3281 helix: 1.53 (0.20), residues: 728 sheet: 0.25 (0.16), residues: 1073 loop : -0.52 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 293 TYR 0.019 0.001 TYR D 74 PHE 0.016 0.001 PHE A 210 TRP 0.017 0.001 TRP H1609 HIS 0.007 0.001 HIS H1442 Details of bonding type rmsd covalent geometry : bond 0.00361 (25363) covalent geometry : angle 0.54749 (34532) SS BOND : bond 0.00463 ( 24) SS BOND : angle 1.59766 ( 48) hydrogen bonds : bond 0.03608 ( 1031) hydrogen bonds : angle 5.26152 ( 2991) link_NAG-ASN : bond 0.00193 ( 4) link_NAG-ASN : angle 1.77285 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 262 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 311 HIS cc_start: 0.6892 (m170) cc_final: 0.6681 (m170) REVERT: G 211 GLU cc_start: 0.6946 (tt0) cc_final: 0.6743 (tt0) REVERT: G 523 GLU cc_start: 0.8216 (pp20) cc_final: 0.7751 (pp20) REVERT: H 1270 LEU cc_start: 0.6783 (pt) cc_final: 0.6270 (tp) REVERT: H 1385 MET cc_start: 0.8512 (tmm) cc_final: 0.8187 (tmm) outliers start: 27 outliers final: 19 residues processed: 278 average time/residue: 0.1545 time to fit residues: 71.4497 Evaluate side-chains 263 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain A residue 640 CYS Chi-restraints excluded: chain B residue 755 ASP Chi-restraints excluded: chain B residue 1297 LEU Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain G residue 3 MET Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 625 THR Chi-restraints excluded: chain H residue 1339 PHE Chi-restraints excluded: chain H residue 1364 LEU Chi-restraints excluded: chain H residue 1449 LEU Chi-restraints excluded: chain H residue 1486 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 44 optimal weight: 7.9990 chunk 222 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 283 optimal weight: 30.0000 chunk 178 optimal weight: 2.9990 chunk 316 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 chunk 216 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 980 HIS B1248 GLN ** H 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.191472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.153128 restraints weight = 34255.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.149418 restraints weight = 58472.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.152025 restraints weight = 52627.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.152232 restraints weight = 30399.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.153258 restraints weight = 27462.765| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25391 Z= 0.136 Angle : 0.538 8.982 34592 Z= 0.279 Chirality : 0.044 0.185 4079 Planarity : 0.004 0.047 4443 Dihedral : 5.296 59.266 3617 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 2.06 % Allowed : 13.71 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 aren not related in a simple way. whole: 0.29 (0.15), residues: 3281 helix: 1.58 (0.20), residues: 728 sheet: 0.27 (0.16), residues: 1062 loop : -0.50 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 293 TYR 0.016 0.001 TYR G 424 PHE 0.015 0.001 PHE A 210 TRP 0.008 0.001 TRP H1590 HIS 0.004 0.001 HIS G 311 Details of bonding type rmsd covalent geometry : bond 0.00329 (25363) covalent geometry : angle 0.53530 (34532) SS BOND : bond 0.00432 ( 24) SS BOND : angle 1.38968 ( 48) hydrogen bonds : bond 0.03194 ( 1031) hydrogen bonds : angle 4.90687 ( 2991) link_NAG-ASN : bond 0.00224 ( 4) link_NAG-ASN : angle 1.82701 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 266 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: C 74 TYR cc_start: 0.7717 (t80) cc_final: 0.7439 (t80) REVERT: A 201 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6952 (mt-10) REVERT: A 311 HIS cc_start: 0.6906 (m170) cc_final: 0.6678 (m170) REVERT: A 584 ASN cc_start: 0.7451 (t0) cc_final: 0.6530 (m-40) REVERT: B 1193 LYS cc_start: 0.5561 (pptt) cc_final: 0.5336 (pptt) REVERT: G 211 GLU cc_start: 0.6923 (tt0) cc_final: 0.6717 (tt0) REVERT: G 296 ASP cc_start: 0.7693 (t70) cc_final: 0.7481 (t0) REVERT: G 523 GLU cc_start: 0.8220 (pp20) cc_final: 0.7765 (pp20) REVERT: H 1270 LEU cc_start: 0.6695 (pt) cc_final: 0.6282 (tp) REVERT: H 1385 MET cc_start: 0.8552 (tmm) cc_final: 0.8223 (tmm) outliers start: 53 outliers final: 31 residues processed: 305 average time/residue: 0.1514 time to fit residues: 77.2791 Evaluate side-chains 277 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 246 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain A residue 640 CYS Chi-restraints excluded: chain B residue 755 ASP Chi-restraints excluded: chain B residue 1297 LEU Chi-restraints excluded: chain B residue 1368 THR Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 625 THR Chi-restraints excluded: chain H residue 890 VAL Chi-restraints excluded: chain H residue 1339 PHE Chi-restraints excluded: chain H residue 1364 LEU Chi-restraints excluded: chain H residue 1449 LEU Chi-restraints excluded: chain H residue 1486 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 35 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 274 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 314 optimal weight: 30.0000 chunk 242 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 282 optimal weight: 30.0000 chunk 194 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 980 HIS ** B 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1451 GLN G 311 HIS ** H 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.189406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.151166 restraints weight = 34374.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.146914 restraints weight = 60447.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.149238 restraints weight = 56558.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.149911 restraints weight = 31747.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.151378 restraints weight = 27612.403| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25391 Z= 0.148 Angle : 0.547 11.158 34592 Z= 0.281 Chirality : 0.044 0.186 4079 Planarity : 0.004 0.048 4443 Dihedral : 5.170 59.357 3617 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.25 % Rotamer: Outliers : 2.14 % Allowed : 15.54 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 aren not related in a simple way. whole: 0.27 (0.15), residues: 3281 helix: 1.58 (0.20), residues: 723 sheet: 0.23 (0.16), residues: 1070 loop : -0.49 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 293 TYR 0.017 0.001 TYR G 424 PHE 0.016 0.001 PHE A 210 TRP 0.021 0.001 TRP H1605 HIS 0.004 0.001 HIS H1442 Details of bonding type rmsd covalent geometry : bond 0.00361 (25363) covalent geometry : angle 0.54284 (34532) SS BOND : bond 0.00543 ( 24) SS BOND : angle 1.74307 ( 48) hydrogen bonds : bond 0.03168 ( 1031) hydrogen bonds : angle 4.78723 ( 2991) link_NAG-ASN : bond 0.00192 ( 4) link_NAG-ASN : angle 1.84951 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 253 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: C 103 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7938 (mp) REVERT: A 201 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7098 (mt-10) REVERT: A 311 HIS cc_start: 0.6880 (m170) cc_final: 0.6653 (m170) REVERT: B 1193 LYS cc_start: 0.5596 (pptt) cc_final: 0.5365 (pptt) REVERT: G 296 ASP cc_start: 0.7473 (t70) cc_final: 0.7248 (t0) REVERT: G 523 GLU cc_start: 0.8106 (pp20) cc_final: 0.7734 (pp20) REVERT: H 1270 LEU cc_start: 0.6589 (pt) cc_final: 0.6229 (tp) outliers start: 55 outliers final: 35 residues processed: 294 average time/residue: 0.1491 time to fit residues: 73.6550 Evaluate side-chains 282 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain A residue 640 CYS Chi-restraints excluded: chain B residue 755 ASP Chi-restraints excluded: chain B residue 1297 LEU Chi-restraints excluded: chain B residue 1368 THR Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain B residue 1399 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 392 HIS Chi-restraints excluded: chain G residue 625 THR Chi-restraints excluded: chain H residue 890 VAL Chi-restraints excluded: chain H residue 1339 PHE Chi-restraints excluded: chain H residue 1364 LEU Chi-restraints excluded: chain H residue 1449 LEU Chi-restraints excluded: chain H residue 1486 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 chunk 246 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 chunk 193 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 980 HIS G 311 HIS ** H 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.190157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.153697 restraints weight = 34389.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.151288 restraints weight = 59669.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.152968 restraints weight = 56231.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.153700 restraints weight = 31440.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.154426 restraints weight = 27250.256| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25391 Z= 0.163 Angle : 0.561 10.083 34592 Z= 0.288 Chirality : 0.044 0.186 4079 Planarity : 0.004 0.049 4443 Dihedral : 5.068 59.349 3617 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.22 % Rotamer: Outliers : 2.30 % Allowed : 16.13 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 aren not related in a simple way. whole: 0.24 (0.15), residues: 3281 helix: 1.57 (0.20), residues: 722 sheet: 0.21 (0.16), residues: 1067 loop : -0.51 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 364 TYR 0.027 0.001 TYR D 74 PHE 0.018 0.002 PHE A 210 TRP 0.010 0.001 TRP B1198 HIS 0.003 0.001 HIS H1442 Details of bonding type rmsd covalent geometry : bond 0.00398 (25363) covalent geometry : angle 0.55440 (34532) SS BOND : bond 0.00619 ( 24) SS BOND : angle 2.27399 ( 48) hydrogen bonds : bond 0.03207 ( 1031) hydrogen bonds : angle 4.74508 ( 2991) link_NAG-ASN : bond 0.00184 ( 4) link_NAG-ASN : angle 1.82190 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 250 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: C 103 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7884 (mp) REVERT: A 201 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7042 (mt-10) REVERT: B 1193 LYS cc_start: 0.5653 (pptt) cc_final: 0.5415 (pptt) REVERT: G 296 ASP cc_start: 0.7611 (t70) cc_final: 0.7360 (t0) REVERT: G 523 GLU cc_start: 0.8161 (pp20) cc_final: 0.7705 (pp20) REVERT: H 1270 LEU cc_start: 0.6595 (pt) cc_final: 0.6254 (tp) REVERT: H 1385 MET cc_start: 0.8482 (tmm) cc_final: 0.8276 (tpp) outliers start: 59 outliers final: 45 residues processed: 296 average time/residue: 0.1465 time to fit residues: 73.4611 Evaluate side-chains 291 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 245 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain A residue 640 CYS Chi-restraints excluded: chain B residue 755 ASP Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 1297 LEU Chi-restraints excluded: chain B residue 1368 THR Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain B residue 1399 LEU Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 372 GLU Chi-restraints excluded: chain G residue 392 HIS Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain H residue 828 VAL Chi-restraints excluded: chain H residue 855 THR Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain H residue 872 LEU Chi-restraints excluded: chain H residue 890 VAL Chi-restraints excluded: chain H residue 909 VAL Chi-restraints excluded: chain H residue 1339 PHE Chi-restraints excluded: chain H residue 1364 LEU Chi-restraints excluded: chain H residue 1449 LEU Chi-restraints excluded: chain H residue 1486 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 117 optimal weight: 40.0000 chunk 274 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 293 optimal weight: 20.0000 chunk 314 optimal weight: 0.0870 chunk 25 optimal weight: 0.2980 chunk 103 optimal weight: 0.9980 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 980 HIS B1268 GLN G 311 HIS ** H 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.192668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.154461 restraints weight = 34205.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.150830 restraints weight = 57535.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.153378 restraints weight = 51885.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.153624 restraints weight = 30004.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.155098 restraints weight = 27105.688| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25391 Z= 0.122 Angle : 0.537 9.474 34592 Z= 0.276 Chirality : 0.043 0.180 4079 Planarity : 0.004 0.048 4443 Dihedral : 4.846 58.529 3617 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 2.06 % Allowed : 16.98 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 aren not related in a simple way. whole: 0.31 (0.15), residues: 3281 helix: 1.63 (0.20), residues: 723 sheet: 0.28 (0.16), residues: 1072 loop : -0.50 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 364 TYR 0.022 0.001 TYR D 74 PHE 0.015 0.001 PHE B1536 TRP 0.018 0.001 TRP H1605 HIS 0.008 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00294 (25363) covalent geometry : angle 0.53252 (34532) SS BOND : bond 0.00467 ( 24) SS BOND : angle 1.70982 ( 48) hydrogen bonds : bond 0.02945 ( 1031) hydrogen bonds : angle 4.60668 ( 2991) link_NAG-ASN : bond 0.00239 ( 4) link_NAG-ASN : angle 1.85577 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 266 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: C 26 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8400 (mt) REVERT: C 103 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7864 (mp) REVERT: D 105 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7577 (mm-30) REVERT: A 20 MET cc_start: 0.7238 (mtt) cc_final: 0.7026 (ptp) REVERT: A 201 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7091 (mt-10) REVERT: A 377 SER cc_start: 0.8587 (t) cc_final: 0.8377 (p) REVERT: B 1562 PHE cc_start: 0.6269 (m-80) cc_final: 0.6064 (m-80) REVERT: G 296 ASP cc_start: 0.7549 (t70) cc_final: 0.7305 (t0) REVERT: G 523 GLU cc_start: 0.8145 (pp20) cc_final: 0.7689 (pp20) REVERT: H 1270 LEU cc_start: 0.6567 (pt) cc_final: 0.6278 (tp) REVERT: H 1385 MET cc_start: 0.8491 (tmm) cc_final: 0.8235 (tpp) outliers start: 53 outliers final: 38 residues processed: 308 average time/residue: 0.1461 time to fit residues: 75.9045 Evaluate side-chains 293 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 755 ASP Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 1297 LEU Chi-restraints excluded: chain B residue 1368 THR Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain B residue 1581 LEU Chi-restraints excluded: chain G residue 66 PHE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 239 TYR Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 392 HIS Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 625 THR Chi-restraints excluded: chain H residue 828 VAL Chi-restraints excluded: chain H residue 855 THR Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain H residue 890 VAL Chi-restraints excluded: chain H residue 909 VAL Chi-restraints excluded: chain H residue 1339 PHE Chi-restraints excluded: chain H residue 1364 LEU Chi-restraints excluded: chain H residue 1449 LEU Chi-restraints excluded: chain H residue 1486 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 178 optimal weight: 4.9990 chunk 291 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 235 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 326 optimal weight: 0.0050 chunk 301 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 292 optimal weight: 0.8980 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS B 980 HIS G 311 HIS H 762 ASN ** H 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.192081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.154471 restraints weight = 34249.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.151321 restraints weight = 58259.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.153758 restraints weight = 51258.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.153626 restraints weight = 32133.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.155115 restraints weight = 29097.928| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25391 Z= 0.137 Angle : 0.548 9.598 34592 Z= 0.283 Chirality : 0.044 0.179 4079 Planarity : 0.004 0.048 4443 Dihedral : 4.744 58.809 3617 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.22 % Rotamer: Outliers : 2.18 % Allowed : 17.53 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 aren not related in a simple way. whole: 0.29 (0.15), residues: 3281 helix: 1.58 (0.20), residues: 728 sheet: 0.32 (0.16), residues: 1068 loop : -0.54 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 364 TYR 0.033 0.001 TYR D 74 PHE 0.017 0.001 PHE A 210 TRP 0.025 0.001 TRP H1605 HIS 0.009 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00332 (25363) covalent geometry : angle 0.54432 (34532) SS BOND : bond 0.00476 ( 24) SS BOND : angle 1.60419 ( 48) hydrogen bonds : bond 0.03004 ( 1031) hydrogen bonds : angle 4.57560 ( 2991) link_NAG-ASN : bond 0.00191 ( 4) link_NAG-ASN : angle 1.87472 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 258 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: C 26 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8405 (mt) REVERT: C 103 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7878 (mp) REVERT: A 201 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7079 (mt-10) REVERT: A 377 SER cc_start: 0.8523 (t) cc_final: 0.8304 (p) REVERT: B 1410 TYR cc_start: 0.6994 (t80) cc_final: 0.6775 (t80) REVERT: G 296 ASP cc_start: 0.7536 (t70) cc_final: 0.7306 (t0) REVERT: G 523 GLU cc_start: 0.8131 (pp20) cc_final: 0.7675 (pp20) REVERT: H 1270 LEU cc_start: 0.6510 (pt) cc_final: 0.6272 (tp) REVERT: H 1385 MET cc_start: 0.8490 (tmm) cc_final: 0.8256 (tpp) outliers start: 56 outliers final: 46 residues processed: 300 average time/residue: 0.1404 time to fit residues: 70.7733 Evaluate side-chains 295 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 247 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 640 CYS Chi-restraints excluded: chain B residue 755 ASP Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 1297 LEU Chi-restraints excluded: chain B residue 1368 THR Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain B residue 1399 LEU Chi-restraints excluded: chain B residue 1581 LEU Chi-restraints excluded: chain G residue 66 PHE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 239 TYR Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 372 GLU Chi-restraints excluded: chain G residue 392 HIS Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 625 THR Chi-restraints excluded: chain H residue 828 VAL Chi-restraints excluded: chain H residue 855 THR Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain H residue 890 VAL Chi-restraints excluded: chain H residue 909 VAL Chi-restraints excluded: chain H residue 1339 PHE Chi-restraints excluded: chain H residue 1364 LEU Chi-restraints excluded: chain H residue 1449 LEU Chi-restraints excluded: chain H residue 1460 TYR Chi-restraints excluded: chain H residue 1486 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 79 optimal weight: 0.8980 chunk 284 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 157 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 23 optimal weight: 0.0000 chunk 119 optimal weight: 40.0000 chunk 126 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 106 optimal weight: 40.0000 chunk 43 optimal weight: 0.0010 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 4 HIS A 311 HIS B 980 HIS G 311 HIS G 584 ASN H 762 ASN ** H 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1305 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.194955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.157643 restraints weight = 34162.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.154834 restraints weight = 57831.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.157049 restraints weight = 50233.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.157109 restraints weight = 31541.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.158212 restraints weight = 28838.889| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25391 Z= 0.100 Angle : 0.528 10.091 34592 Z= 0.273 Chirality : 0.043 0.169 4079 Planarity : 0.004 0.048 4443 Dihedral : 4.492 57.745 3617 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % Rotamer: Outliers : 1.56 % Allowed : 18.47 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 aren not related in a simple way. whole: 0.42 (0.15), residues: 3281 helix: 1.63 (0.20), residues: 728 sheet: 0.49 (0.16), residues: 1062 loop : -0.50 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 364 TYR 0.028 0.001 TYR D 74 PHE 0.015 0.001 PHE A 507 TRP 0.017 0.001 TRP H1605 HIS 0.004 0.000 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00232 (25363) covalent geometry : angle 0.52463 (34532) SS BOND : bond 0.00389 ( 24) SS BOND : angle 1.44721 ( 48) hydrogen bonds : bond 0.02678 ( 1031) hydrogen bonds : angle 4.42122 ( 2991) link_NAG-ASN : bond 0.00274 ( 4) link_NAG-ASN : angle 1.94717 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 270 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: C 18 ASP cc_start: 0.6038 (p0) cc_final: 0.5769 (p0) REVERT: C 26 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8389 (mt) REVERT: C 103 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7768 (mp) REVERT: D 105 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7537 (mm-30) REVERT: A 201 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7102 (mt-10) REVERT: G 20 MET cc_start: 0.7008 (ptt) cc_final: 0.6751 (ptt) REVERT: G 296 ASP cc_start: 0.7409 (t70) cc_final: 0.7199 (t0) outliers start: 40 outliers final: 29 residues processed: 300 average time/residue: 0.1321 time to fit residues: 66.6549 Evaluate side-chains 281 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 250 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 640 CYS Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 1297 LEU Chi-restraints excluded: chain B residue 1368 THR Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain B residue 1399 LEU Chi-restraints excluded: chain B residue 1581 LEU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 239 TYR Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 392 HIS Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 584 ASN Chi-restraints excluded: chain G residue 625 THR Chi-restraints excluded: chain H residue 762 ASN Chi-restraints excluded: chain H residue 828 VAL Chi-restraints excluded: chain H residue 855 THR Chi-restraints excluded: chain H residue 890 VAL Chi-restraints excluded: chain H residue 909 VAL Chi-restraints excluded: chain H residue 1364 LEU Chi-restraints excluded: chain H residue 1460 TYR Chi-restraints excluded: chain H residue 1486 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 5 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 226 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 201 optimal weight: 0.9990 chunk 313 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 326 optimal weight: 0.0070 chunk 70 optimal weight: 0.5980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 311 HIS G 584 ASN H 762 ASN ** H 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1327 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.186010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.146162 restraints weight = 34605.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.142240 restraints weight = 58660.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.144753 restraints weight = 53601.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.144794 restraints weight = 31347.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.146180 restraints weight = 28573.014| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25391 Z= 0.107 Angle : 0.545 10.703 34592 Z= 0.279 Chirality : 0.043 0.172 4079 Planarity : 0.004 0.047 4443 Dihedral : 4.447 58.061 3617 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Rotamer: Outliers : 1.29 % Allowed : 19.48 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 aren not related in a simple way. whole: 0.45 (0.15), residues: 3281 helix: 1.62 (0.20), residues: 731 sheet: 0.52 (0.16), residues: 1056 loop : -0.48 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 364 TYR 0.041 0.001 TYR B1410 PHE 0.014 0.001 PHE A 507 TRP 0.017 0.001 TRP H1605 HIS 0.004 0.001 HIS G 311 Details of bonding type rmsd covalent geometry : bond 0.00251 (25363) covalent geometry : angle 0.54143 (34532) SS BOND : bond 0.00388 ( 24) SS BOND : angle 1.42458 ( 48) hydrogen bonds : bond 0.02723 ( 1031) hydrogen bonds : angle 4.37994 ( 2991) link_NAG-ASN : bond 0.00226 ( 4) link_NAG-ASN : angle 1.90286 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 257 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: C 18 ASP cc_start: 0.6248 (p0) cc_final: 0.6004 (p0) REVERT: C 26 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8406 (mt) REVERT: D 105 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7521 (mm-30) REVERT: A 201 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7085 (mt-10) REVERT: G 20 MET cc_start: 0.7010 (ptt) cc_final: 0.6716 (ptt) REVERT: G 296 ASP cc_start: 0.7497 (t70) cc_final: 0.7279 (t0) outliers start: 33 outliers final: 27 residues processed: 285 average time/residue: 0.1241 time to fit residues: 59.5792 Evaluate side-chains 277 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 249 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 640 CYS Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 1297 LEU Chi-restraints excluded: chain B residue 1368 THR Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain B residue 1399 LEU Chi-restraints excluded: chain B residue 1581 LEU Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 239 TYR Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 392 HIS Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 625 THR Chi-restraints excluded: chain H residue 828 VAL Chi-restraints excluded: chain H residue 855 THR Chi-restraints excluded: chain H residue 890 VAL Chi-restraints excluded: chain H residue 909 VAL Chi-restraints excluded: chain H residue 1364 LEU Chi-restraints excluded: chain H residue 1460 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 211 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 291 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 270 optimal weight: 50.0000 chunk 223 optimal weight: 0.0870 chunk 8 optimal weight: 0.0070 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS G 311 HIS ** H 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.184927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.147124 restraints weight = 34677.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.145352 restraints weight = 56395.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.146702 restraints weight = 56288.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.147272 restraints weight = 32091.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.147992 restraints weight = 28106.737| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25391 Z= 0.128 Angle : 0.552 10.995 34592 Z= 0.283 Chirality : 0.044 0.175 4079 Planarity : 0.004 0.048 4443 Dihedral : 4.454 58.100 3617 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 1.48 % Allowed : 19.40 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 aren not related in a simple way. whole: 0.40 (0.15), residues: 3281 helix: 1.59 (0.20), residues: 731 sheet: 0.48 (0.16), residues: 1055 loop : -0.51 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 364 TYR 0.030 0.001 TYR B1410 PHE 0.015 0.001 PHE B1536 TRP 0.015 0.001 TRP B1198 HIS 0.018 0.001 HIS G 311 Details of bonding type rmsd covalent geometry : bond 0.00309 (25363) covalent geometry : angle 0.54911 (34532) SS BOND : bond 0.00401 ( 24) SS BOND : angle 1.43800 ( 48) hydrogen bonds : bond 0.02821 ( 1031) hydrogen bonds : angle 4.38461 ( 2991) link_NAG-ASN : bond 0.00177 ( 4) link_NAG-ASN : angle 1.88269 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3469.70 seconds wall clock time: 61 minutes 1.05 seconds (3661.05 seconds total)