Starting phenix.real_space_refine on Thu Mar 6 06:44:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kby_37087/03_2025/8kby_37087.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kby_37087/03_2025/8kby_37087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kby_37087/03_2025/8kby_37087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kby_37087/03_2025/8kby_37087.map" model { file = "/net/cci-nas-00/data/ceres_data/8kby_37087/03_2025/8kby_37087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kby_37087/03_2025/8kby_37087.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 3121 2.51 5 N 934 2.21 5 O 980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5050 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 5050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 5050 Classifications: {'peptide': 830} Incomplete info: {'truncation_to_alanine': 446} Link IDs: {'PTRANS': 46, 'TRANS': 783} Chain breaks: 26 Unresolved chain link angles: 29 Unresolved non-hydrogen bonds: 1646 Unresolved non-hydrogen angles: 2113 Unresolved non-hydrogen dihedrals: 1370 Unresolved non-hydrogen chiralities: 161 Planarities with less than four sites: {'GLN:plan1': 23, 'ASP:plan': 24, 'TYR:plan': 15, 'ASN:plan1': 6, 'TRP:plan': 7, 'HIS:plan': 17, 'PHE:plan': 17, 'GLU:plan': 39, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 878 Time building chain proxies: 6.52, per 1000 atoms: 1.29 Number of scatterers: 5050 At special positions: 0 Unit cell: (54.4, 96.05, 162.35, 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 15 16.00 O 980 8.00 N 934 7.00 C 3121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 752.6 milliseconds 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1592 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 4 sheets defined 14.0% alpha, 46.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'B' and resid 292 through 304 removed outlier: 4.642A pdb=" N GLN B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 462 Processing helix chain 'B' and resid 600 through 609 removed outlier: 4.376A pdb=" N LEU B 606 " --> pdb=" O ARG B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 807 Processing helix chain 'B' and resid 828 through 841 removed outlier: 4.076A pdb=" N ILE B 833 " --> pdb=" O VAL B 829 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR B 834 " --> pdb=" O TYR B 830 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN B 838 " --> pdb=" O TYR B 834 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN B 839 " --> pdb=" O ASN B 835 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU B 841 " --> pdb=" O ILE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 1082 through 1093 removed outlier: 3.887A pdb=" N LEU B1093 " --> pdb=" O LEU B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1224 through 1237 Processing helix chain 'B' and resid 1591 through 1591 No H-bonds generated for 'chain 'B' and resid 1591 through 1591' Processing helix chain 'B' and resid 1595 through 1607 Processing helix chain 'B' and resid 1691 through 1699 Processing helix chain 'B' and resid 1722 through 1729 Processing sheet with id=A, first strand: chain 'B' and resid 173 through 176 removed outlier: 7.738A pdb=" N ASP B 173 " --> pdb=" O ASP B 202 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ASP B 202 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 175 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR B 200 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU B 198 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU B 229 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR B 200 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU B 227 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP B 202 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LYS B 225 " --> pdb=" O ASP B 202 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 223 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 265 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LYS B 225 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL B 263 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU B 227 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU B 261 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 229 " --> pdb=" O MET B 259 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET B 259 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU B 260 " --> pdb=" O GLN B 281 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN B 281 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET B 262 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 279 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS B 264 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLU B 277 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU B 426 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL B 278 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS B 428 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLY B 280 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N THR B 430 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 282 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER B 425 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU B 501 " --> pdb=" O SER B 425 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 427 " --> pdb=" O TRP B 499 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N TRP B 499 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET B 429 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU B 497 " --> pdb=" O MET B 429 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU B 431 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 495 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN B 496 " --> pdb=" O HIS B 516 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N HIS B 516 " --> pdb=" O GLN B 496 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 514 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N SER B 512 " --> pdb=" O GLU B 500 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B 502 " --> pdb=" O THR B 510 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG B 509 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B 564 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR B 511 " --> pdb=" O GLN B 562 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLN B 562 " --> pdb=" O THR B 511 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N MET B 513 " --> pdb=" O HIS B 560 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 558 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA B 556 " --> pdb=" O PHE B 517 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N HIS B 557 " --> pdb=" O ASP B 587 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP B 587 " --> pdb=" O HIS B 557 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG B 559 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA B 585 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR B 561 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU B 583 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 563 " --> pdb=" O HIS B 581 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N HIS B 581 " --> pdb=" O ILE B 563 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 565 " --> pdb=" O HIS B 579 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N HIS B 579 " --> pdb=" O ARG B 565 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N GLU B 629 " --> pdb=" O CYS B 580 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N SER B 582 " --> pdb=" O GLU B 629 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLN B 631 " --> pdb=" O SER B 582 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU B 584 " --> pdb=" O GLN B 631 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B 633 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 586 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG B 635 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 588 " --> pdb=" O ARG B 635 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER B 637 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N GLN B 630 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER B 684 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU B 636 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE B 678 " --> pdb=" O LEU B 636 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLN B 677 " --> pdb=" O THR B 697 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR B 697 " --> pdb=" O GLN B 677 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG B 679 " --> pdb=" O GLU B 695 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 695 " --> pdb=" O ARG B 679 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 681 " --> pdb=" O HIS B 693 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N HIS B 693 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU B 696 " --> pdb=" O VAL B 736 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 736 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B 735 " --> pdb=" O ILE B 816 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR B 739 " --> pdb=" O SER B 812 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N SER B 812 " --> pdb=" O THR B 739 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER B 927 " --> pdb=" O CYS B 811 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 813 " --> pdb=" O SER B 927 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 929 " --> pdb=" O LEU B 813 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 931 " --> pdb=" O VAL B 815 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE B 926 " --> pdb=" O SER B 971 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER B 971 " --> pdb=" O PHE B 926 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 969 " --> pdb=" O THR B 928 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 967 " --> pdb=" O VAL B 930 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU B 985 " --> pdb=" O THR B 966 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 968 " --> pdb=" O CYS B 983 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS B 983 " --> pdb=" O PHE B 968 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL B 970 " --> pdb=" O TYR B 981 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR B 981 " --> pdb=" O VAL B 970 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 980 " --> pdb=" O ILE B1052 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B1052 " --> pdb=" O GLY B 980 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE B 982 " --> pdb=" O VAL B1050 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 984 " --> pdb=" O THR B1048 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA B 986 " --> pdb=" O LEU B1046 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU B1046 " --> pdb=" O ALA B 986 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG B1068 " --> pdb=" O SER B1047 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B1049 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR B1066 " --> pdb=" O ALA B1049 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N HIS B1053 " --> pdb=" O GLU B1062 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU B1062 " --> pdb=" O HIS B1053 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASP B1055 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B1060 " --> pdb=" O ASP B1055 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR B1107 " --> pdb=" O LYS B1061 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N PHE B1063 " --> pdb=" O THR B1107 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE B1109 " --> pdb=" O PHE B1063 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N VAL B1065 " --> pdb=" O ILE B1109 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE B1111 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LEU B1067 " --> pdb=" O ILE B1111 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N HIS B1113 " --> pdb=" O LEU B1067 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N LEU B1069 " --> pdb=" O HIS B1113 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N HIS B1115 " --> pdb=" O LEU B1069 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR B1110 " --> pdb=" O ILE B1145 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE B1145 " --> pdb=" O THR B1110 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU B1112 " --> pdb=" O SER B1143 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B1114 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B1141 " --> pdb=" O THR B1114 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR B1138 " --> pdb=" O ASP B1159 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP B1159 " --> pdb=" O THR B1138 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR B1140 " --> pdb=" O ILE B1157 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE B1157 " --> pdb=" O THR B1140 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER B1142 " --> pdb=" O ARG B1155 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B1155 " --> pdb=" O SER B1142 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN B1144 " --> pdb=" O LEU B1153 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU B1153 " --> pdb=" O ASN B1144 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE B1146 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR B1151 " --> pdb=" O ILE B1146 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE B1156 " --> pdb=" O LEU B1191 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B1191 " --> pdb=" O PHE B1156 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B1158 " --> pdb=" O LEU B1189 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU B1189 " --> pdb=" O LEU B1158 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU B1190 " --> pdb=" O SER B1214 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER B1214 " --> pdb=" O GLU B1190 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL B1192 " --> pdb=" O ARG B1212 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ARG B1212 " --> pdb=" O VAL B1192 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS B1194 " --> pdb=" O GLU B1210 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU B1210 " --> pdb=" O LYS B1194 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ARG B1418 " --> pdb=" O PHE B1209 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU B1211 " --> pdb=" O ARG B1418 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VAL B1420 " --> pdb=" O LEU B1211 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N CYS B1213 " --> pdb=" O VAL B1420 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ARG B1422 " --> pdb=" O CYS B1213 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASN B1215 " --> pdb=" O ARG B1422 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N THR B1417 " --> pdb=" O VAL B1495 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B1495 " --> pdb=" O THR B1417 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VAL B1419 " --> pdb=" O HIS B1493 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS B1493 " --> pdb=" O VAL B1419 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU B1421 " --> pdb=" O PHE B1491 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE B1491 " --> pdb=" O LEU B1421 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER B1490 " --> pdb=" O ILE B1522 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE B1522 " --> pdb=" O SER B1490 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN B1492 " --> pdb=" O VAL B1520 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL B1520 " --> pdb=" O GLN B1492 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLU B1494 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ARG B1518 " --> pdb=" O GLU B1494 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B1516 " --> pdb=" O HIS B1564 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N HIS B1564 " --> pdb=" O LEU B1516 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N ARG B1518 " --> pdb=" O ALA B1562 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA B1562 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N VAL B1520 " --> pdb=" O ILE B1560 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE B1560 " --> pdb=" O VAL B1520 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE B1522 " --> pdb=" O LEU B1558 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU B1558 " --> pdb=" O ILE B1522 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR B1559 " --> pdb=" O SER B1581 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER B1581 " --> pdb=" O THR B1559 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LYS B1561 " --> pdb=" O ARG B1579 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG B1579 " --> pdb=" O LYS B1561 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEU B1563 " --> pdb=" O CYS B1577 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N CYS B1577 " --> pdb=" O LEU B1563 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU B1666 " --> pdb=" O CYS B1576 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B1578 " --> pdb=" O GLU B1666 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ARG B1668 " --> pdb=" O LEU B1578 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B1580 " --> pdb=" O ARG B1668 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N THR B1670 " --> pdb=" O VAL B1580 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N LEU B1582 " --> pdb=" O THR B1670 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE B1667 " --> pdb=" O CYS B1714 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N CYS B1714 " --> pdb=" O PHE B1667 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B1669 " --> pdb=" O LEU B1712 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU B1712 " --> pdb=" O PHE B1669 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'B' and resid 536 through 543 removed outlier: 12.200A pdb=" N TYR B 536 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N GLU B 524 " --> pdb=" O TYR B 536 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU B 538 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 522 " --> pdb=" O GLU B 538 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B 540 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU B 520 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N GLN B 519 " --> pdb=" O THR B 493 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N THR B 493 " --> pdb=" O GLN B 519 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLU B 521 " --> pdb=" O THR B 491 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N THR B 491 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU B 523 " --> pdb=" O ARG B 489 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ARG B 489 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL B 488 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU B 438 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 436 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLY B 492 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL B 434 " --> pdb=" O GLY B 492 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N LEU B 285 " --> pdb=" O GLY B 433 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N THR B 435 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N LEU B 287 " --> pdb=" O THR B 435 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR B 437 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU B 289 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU B 439 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N SER B 284 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER B 256 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N HIS B 286 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 9.589A pdb=" N SER B 254 " --> pdb=" O HIS B 286 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N LEU B 288 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N ILE B 252 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 12.228A pdb=" N THR B 290 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 13.602A pdb=" N LEU B 250 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU B 250 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N TYR B 236 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE B 252 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B 234 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER B 254 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 232 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG B 194 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 234 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N GLU B 192 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL B 193 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N HIS B 180 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N VAL B 195 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 178 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'B' and resid 591 through 597 removed outlier: 4.458A pdb=" N ALA B 641 " --> pdb=" O PHE B 591 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA B 593 " --> pdb=" O ALA B 641 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 643 " --> pdb=" O ALA B 593 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 595 " --> pdb=" O LEU B 643 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 645 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU B 597 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA B 641 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU B 673 " --> pdb=" O ALA B 641 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 643 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 671 " --> pdb=" O LEU B 643 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 645 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU B 669 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLN B 668 " --> pdb=" O GLU B 706 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 706 " --> pdb=" O GLN B 668 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU B 672 " --> pdb=" O HIS B 702 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N HIS B 702 " --> pdb=" O GLU B 672 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N SER B 674 " --> pdb=" O ASP B 700 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N ASP B 700 " --> pdb=" O SER B 674 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU B 701 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL B 718 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLY B 703 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU B 716 " --> pdb=" O GLY B 703 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR B 705 " --> pdb=" O PRO B 714 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N CYS B 715 " --> pdb=" O PHE B 823 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE B 823 " --> pdb=" O CYS B 715 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ARG B 717 " --> pdb=" O HIS B 821 " (cutoff:3.500A) removed outlier: 9.867A pdb=" N HIS B 821 " --> pdb=" O ARG B 717 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER B 719 " --> pdb=" O SER B 819 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N SER B 819 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL B 820 " --> pdb=" O LYS B 934 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG B 936 " --> pdb=" O VAL B 820 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ILE B 822 " --> pdb=" O ARG B 936 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR B 938 " --> pdb=" O ILE B 822 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N LEU B 824 " --> pdb=" O THR B 938 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET B 962 " --> pdb=" O GLY B 935 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE B 937 " --> pdb=" O LEU B 960 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU B 960 " --> pdb=" O ILE B 937 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA B 939 " --> pdb=" O LEU B 958 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N LEU B 958 " --> pdb=" O ALA B 939 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU B 958 " --> pdb=" O HIS B 993 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N HIS B 993 " --> pdb=" O LEU B 958 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N LEU B 960 " --> pdb=" O LEU B 991 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N LEU B 991 " --> pdb=" O LEU B 960 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N MET B 962 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ALA B 989 " --> pdb=" O MET B 962 " (cutoff:3.500A) removed outlier: 11.556A pdb=" N ALA B 989 " --> pdb=" O PRO B1023 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B 991 " --> pdb=" O ILE B1021 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N HIS B 993 " --> pdb=" O PRO B1019 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N THR B1020 " --> pdb=" O ARG B1075 " (cutoff:3.500A) removed outlier: 10.744A pdb=" N ARG B1075 " --> pdb=" O THR B1020 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR B1022 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR B1073 " --> pdb=" O TYR B1022 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N SER B1120 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N HIS B1076 " --> pdb=" O SER B1120 " (cutoff:3.500A) removed outlier: 13.226A pdb=" N ASP B1122 " --> pdb=" O HIS B1076 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N CYS B1119 " --> pdb=" O ALA B1136 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA B1136 " --> pdb=" O CYS B1119 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR B1123 " --> pdb=" O VAL B1132 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL B1132 " --> pdb=" O TYR B1123 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ARG B1131 " --> pdb=" O SER B1166 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER B1166 " --> pdb=" O ARG B1131 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B1135 " --> pdb=" O ALA B1162 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B1162 " --> pdb=" O THR B1135 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B1163 " --> pdb=" O LEU B1184 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B1184 " --> pdb=" O LEU B1163 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B1165 " --> pdb=" O CYS B1182 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N CYS B1182 " --> pdb=" O LEU B1165 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B1183 " --> pdb=" O HIS B1221 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS B1221 " --> pdb=" O VAL B1183 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL B1424 " --> pdb=" O VAL B1218 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B1220 " --> pdb=" O VAL B1424 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B1426 " --> pdb=" O VAL B1220 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N SER B1222 " --> pdb=" O LEU B1426 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N TRP B1428 " --> pdb=" O SER B1222 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B1486 " --> pdb=" O VAL B1424 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU B1426 " --> pdb=" O ILE B1484 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE B1484 " --> pdb=" O LEU B1426 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TRP B1428 " --> pdb=" O MET B1482 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLU B1483 " --> pdb=" O ARG B1529 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B1529 " --> pdb=" O GLU B1483 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU B1527 " --> pdb=" O GLN B1485 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 1539 through 1542 removed outlier: 5.264A pdb=" N PHE B1540 " --> pdb=" O ASN B1588 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN B1588 " --> pdb=" O PHE B1540 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N TYR B1542 " --> pdb=" O ARG B1586 " (cutoff:3.500A) removed outlier: 9.865A pdb=" N ARG B1586 " --> pdb=" O TYR B1542 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU B1585 " --> pdb=" O PRO B1674 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TRP B1676 " --> pdb=" O LEU B1585 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU B1587 " --> pdb=" O TRP B1676 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B1589 " --> pdb=" O ASP B1678 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL B1673 " --> pdb=" O LEU B1709 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B1709 " --> pdb=" O VAL B1673 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B1675 " --> pdb=" O LEU B1707 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU B1707 " --> pdb=" O ILE B1675 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER B1705 " --> pdb=" O LEU B1677 " (cutoff:3.500A) 124 hydrogen bonds defined for protein. 354 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: 2.31 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1550 1.33 - 1.45: 568 1.45 - 1.57: 2942 1.57 - 1.69: 0 1.69 - 1.81: 17 Bond restraints: 5077 Sorted by residual: bond pdb=" CA ARG B 646 " pdb=" C ARG B 646 " ideal model delta sigma weight residual 1.522 1.495 0.026 1.21e-02 6.83e+03 4.72e+00 bond pdb=" N LEU B 673 " pdb=" CA LEU B 673 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.51e+00 bond pdb=" N ARG B 670 " pdb=" CA ARG B 670 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.19e-02 7.06e+03 4.32e+00 bond pdb=" N LEU B 671 " pdb=" CA LEU B 671 " ideal model delta sigma weight residual 1.464 1.437 0.027 1.30e-02 5.92e+03 4.18e+00 bond pdb=" C LEU B 600 " pdb=" O LEU B 600 " ideal model delta sigma weight residual 1.237 1.214 0.023 1.19e-02 7.06e+03 3.60e+00 ... (remaining 5072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 6820 2.49 - 4.98: 118 4.98 - 7.47: 17 7.47 - 9.97: 4 9.97 - 12.46: 4 Bond angle restraints: 6963 Sorted by residual: angle pdb=" N ALA B 599 " pdb=" CA ALA B 599 " pdb=" C ALA B 599 " ideal model delta sigma weight residual 108.76 121.22 -12.46 1.58e+00 4.01e-01 6.22e+01 angle pdb=" C GLN B 677 " pdb=" CA GLN B 677 " pdb=" CB GLN B 677 " ideal model delta sigma weight residual 116.34 105.75 10.59 1.40e+00 5.10e-01 5.72e+01 angle pdb=" N ARG B 670 " pdb=" CA ARG B 670 " pdb=" C ARG B 670 " ideal model delta sigma weight residual 108.34 118.41 -10.07 1.64e+00 3.72e-01 3.77e+01 angle pdb=" N LEU B 671 " pdb=" CA LEU B 671 " pdb=" C LEU B 671 " ideal model delta sigma weight residual 109.62 101.58 8.04 1.50e+00 4.44e-01 2.88e+01 angle pdb=" N GLN B 677 " pdb=" CA GLN B 677 " pdb=" C GLN B 677 " ideal model delta sigma weight residual 108.00 115.74 -7.74 1.48e+00 4.57e-01 2.74e+01 ... (remaining 6958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 2784 17.33 - 34.67: 174 34.67 - 52.00: 44 52.00 - 69.34: 4 69.34 - 86.67: 6 Dihedral angle restraints: 3012 sinusoidal: 610 harmonic: 2402 Sorted by residual: dihedral pdb=" CA GLU B1170 " pdb=" C GLU B1170 " pdb=" N VAL B1171 " pdb=" CA VAL B1171 " ideal model delta harmonic sigma weight residual 180.00 -156.47 -23.53 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ALA B 989 " pdb=" C ALA B 989 " pdb=" N THR B 990 " pdb=" CA THR B 990 " ideal model delta harmonic sigma weight residual 180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA SER B1425 " pdb=" C SER B1425 " pdb=" N LEU B1426 " pdb=" CA LEU B1426 " ideal model delta harmonic sigma weight residual 180.00 159.42 20.58 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 3009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 670 0.047 - 0.093: 195 0.093 - 0.140: 55 0.140 - 0.187: 5 0.187 - 0.233: 2 Chirality restraints: 927 Sorted by residual: chirality pdb=" CA ALA B 599 " pdb=" N ALA B 599 " pdb=" C ALA B 599 " pdb=" CB ALA B 599 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ARG B 679 " pdb=" N ARG B 679 " pdb=" C ARG B 679 " pdb=" CB ARG B 679 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA LEU B 673 " pdb=" N LEU B 673 " pdb=" C LEU B 673 " pdb=" CB LEU B 673 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.97e-01 ... (remaining 924 not shown) Planarity restraints: 925 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B1092 " -0.013 2.00e-02 2.50e+03 1.59e-02 4.41e+00 pdb=" CG PHE B1092 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B1092 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B1092 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B1092 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B1092 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B1092 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 668 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C GLN B 668 " 0.032 2.00e-02 2.50e+03 pdb=" O GLN B 668 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 669 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 713 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO B 714 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 714 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 714 " 0.022 5.00e-02 4.00e+02 ... (remaining 922 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1511 2.81 - 3.33: 4725 3.33 - 3.86: 7405 3.86 - 4.38: 7877 4.38 - 4.90: 13622 Nonbonded interactions: 35140 Sorted by model distance: nonbonded pdb=" O LEU B1604 " pdb=" N ILE B1608 " model vdw 2.288 3.120 nonbonded pdb=" O SER B 819 " pdb=" OG SER B 819 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR B 834 " pdb=" N ASP B1097 " model vdw 2.300 3.120 nonbonded pdb=" OD1 ASN B1215 " pdb=" N ASN B1216 " model vdw 2.346 3.120 nonbonded pdb=" N ASP B1179 " pdb=" OD1 ASP B1179 " model vdw 2.388 3.120 ... (remaining 35135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.890 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4478 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 : 0.003 0.033 5077 Z= 0.238 Angle : 0.910 12.457 6963 Z= 0.541 Chirality : 0.047 0.233 927 Planarity : 0.004 0.039 925 Dihedral : 14.414 86.670 1420 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.24 % Favored : 87.37 % Rotamer: Outliers : 0.00 % Allowed : 26.97 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.87 (0.25), residues: 776 helix: -0.38 (0.52), residues: 106 sheet: -3.95 (0.45), residues: 62 loop : -4.09 (0.20), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 499 HIS 0.003 0.001 HIS B 560 PHE 0.037 0.002 PHE B1092 TYR 0.012 0.001 TYR B 834 ARG 0.006 0.001 ARG B1586 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.570 Fit side-chains REVERT: B 1210 GLU cc_start: 0.6753 (tm-30) cc_final: 0.6071 (tm-30) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1623 time to fit residues: 7.5837 Evaluate side-chains 23 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 34 optimal weight: 0.1980 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5220 r_free = 0.5220 target = 0.210155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4987 r_free = 0.4987 target = 0.182832 restraints weight = 7339.118| |-----------------------------------------------------------------------------| r_work (start): 0.4969 rms_B_bonded: 2.46 r_work: 0.4819 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5077 Z= 0.212 Angle : 0.723 10.380 6963 Z= 0.378 Chirality : 0.046 0.192 927 Planarity : 0.004 0.039 925 Dihedral : 6.322 24.136 826 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.69 % Favored : 85.31 % Rotamer: Outliers : 4.61 % Allowed : 24.01 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.25), residues: 776 helix: -0.50 (0.50), residues: 109 sheet: -3.43 (0.54), residues: 59 loop : -4.03 (0.20), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 499 HIS 0.006 0.001 HIS B1115 PHE 0.023 0.002 PHE B 634 TYR 0.012 0.002 TYR B1022 ARG 0.003 0.001 ARG B1155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.551 Fit side-chains REVERT: B 1103 TYR cc_start: 0.5167 (OUTLIER) cc_final: 0.3580 (t80) REVERT: B 1193 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6335 (mp) outliers start: 14 outliers final: 8 residues processed: 36 average time/residue: 0.1144 time to fit residues: 6.3525 Evaluate side-chains 32 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1086 HIS Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1609 ASN Chi-restraints excluded: chain B residue 1612 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 44 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 55 optimal weight: 0.0980 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 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5119 r_free = 0.5119 target = 0.199732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.175243 restraints weight = 7498.958| |-----------------------------------------------------------------------------| r_work (start): 0.4884 rms_B_bonded: 2.18 r_work: 0.4718 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 5077 Z= 0.443 Angle : 0.922 9.465 6963 Z= 0.493 Chirality : 0.052 0.288 927 Planarity : 0.006 0.067 925 Dihedral : 7.698 27.480 826 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.01 % Favored : 78.99 % Rotamer: Outliers : 9.87 % Allowed : 21.05 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.24), residues: 776 helix: -1.21 (0.47), residues: 108 sheet: -3.82 (0.51), residues: 58 loop : -4.31 (0.20), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 499 HIS 0.007 0.002 HIS B1115 PHE 0.059 0.004 PHE B 634 TYR 0.021 0.003 TYR B 834 ARG 0.004 0.001 ARG B1586 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 23 time to evaluate : 0.587 Fit side-chains REVERT: B 228 GLN cc_start: 0.5109 (OUTLIER) cc_final: 0.4672 (tt0) REVERT: B 694 LEU cc_start: 0.5538 (OUTLIER) cc_final: 0.4989 (mp) REVERT: B 961 ASP cc_start: 0.6386 (OUTLIER) cc_final: 0.6044 (m-30) REVERT: B 1156 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7135 (m-10) outliers start: 30 outliers final: 18 residues processed: 50 average time/residue: 0.1559 time to fit residues: 12.8912 Evaluate side-chains 44 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 22 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 961 ASP Chi-restraints excluded: chain B residue 966 THR Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1052 ILE Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1110 THR Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain B residue 1211 LEU Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1609 ASN Chi-restraints excluded: chain B residue 1612 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 76 optimal weight: 0.0770 chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 46 optimal weight: 0.0670 chunk 21 optimal weight: 0.7980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5204 r_free = 0.5204 target = 0.208772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.182448 restraints weight = 7482.508| |-----------------------------------------------------------------------------| r_work (start): 0.4963 rms_B_bonded: 2.42 r_work: 0.4797 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5077 Z= 0.187 Angle : 0.677 8.119 6963 Z= 0.364 Chirality : 0.045 0.177 927 Planarity : 0.004 0.044 925 Dihedral : 6.476 23.986 826 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer: Outliers : 6.91 % Allowed : 25.66 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.25), residues: 776 helix: -0.43 (0.50), residues: 102 sheet: -3.32 (0.56), residues: 59 loop : -4.24 (0.20), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 499 HIS 0.005 0.001 HIS B1115 PHE 0.024 0.002 PHE B 634 TYR 0.012 0.002 TYR B 834 ARG 0.003 0.001 ARG B1075 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 29 time to evaluate : 0.616 Fit side-chains REVERT: B 228 GLN cc_start: 0.5035 (OUTLIER) cc_final: 0.4640 (tt0) REVERT: B 1062 GLU cc_start: 0.5381 (OUTLIER) cc_final: 0.5143 (tm-30) REVERT: B 1193 ILE cc_start: 0.6815 (OUTLIER) cc_final: 0.6572 (mp) outliers start: 21 outliers final: 12 residues processed: 46 average time/residue: 0.1562 time to fit residues: 10.6848 Evaluate side-chains 40 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1086 HIS Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1609 ASN Chi-restraints excluded: chain B residue 1612 VAL Chi-restraints excluded: chain B residue 1677 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 34 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5078 r_free = 0.5078 target = 0.197107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.172897 restraints weight = 7731.555| |-----------------------------------------------------------------------------| r_work (start): 0.4842 rms_B_bonded: 2.16 r_work: 0.4649 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 5077 Z= 0.517 Angle : 1.038 11.381 6963 Z= 0.553 Chirality : 0.055 0.301 927 Planarity : 0.007 0.079 925 Dihedral : 8.499 29.442 826 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 24.23 % Favored : 75.64 % Rotamer: Outliers : 9.87 % Allowed : 24.34 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.61 (0.24), residues: 776 helix: -1.45 (0.46), residues: 102 sheet: -3.98 (0.55), residues: 55 loop : -4.57 (0.19), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 499 HIS 0.009 0.002 HIS B1115 PHE 0.072 0.005 PHE B 634 TYR 0.023 0.003 TYR B 834 ARG 0.007 0.001 ARG B1586 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 23 time to evaluate : 0.506 Fit side-chains REVERT: B 228 GLN cc_start: 0.5399 (OUTLIER) cc_final: 0.5020 (tt0) REVERT: B 1156 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7350 (m-80) REVERT: B 1193 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.6850 (mp) outliers start: 30 outliers final: 16 residues processed: 50 average time/residue: 0.1016 time to fit residues: 7.9059 Evaluate side-chains 42 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 23 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 966 THR Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1052 ILE Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1211 LEU Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1609 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 77 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5260 r_free = 0.5260 target = 0.218043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.190761 restraints weight = 7384.848| |-----------------------------------------------------------------------------| r_work (start): 0.5013 rms_B_bonded: 2.33 r_work: 0.4878 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5077 Z= 0.172 Angle : 0.678 9.801 6963 Z= 0.362 Chirality : 0.044 0.171 927 Planarity : 0.004 0.056 925 Dihedral : 6.472 26.377 826 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.02 % Favored : 86.98 % Rotamer: Outliers : 5.92 % Allowed : 28.95 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.06 (0.25), residues: 776 helix: -0.63 (0.50), residues: 102 sheet: -3.43 (0.51), residues: 67 loop : -4.26 (0.20), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 499 HIS 0.005 0.001 HIS B 560 PHE 0.018 0.002 PHE B 634 TYR 0.015 0.002 TYR B 834 ARG 0.004 0.001 ARG B1075 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 26 time to evaluate : 0.457 Fit side-chains REVERT: B 228 GLN cc_start: 0.5056 (OUTLIER) cc_final: 0.4679 (tt0) REVERT: B 1062 GLU cc_start: 0.5522 (OUTLIER) cc_final: 0.5312 (tm-30) outliers start: 18 outliers final: 11 residues processed: 43 average time/residue: 0.1127 time to fit residues: 7.5553 Evaluate side-chains 37 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1541 LEU Chi-restraints excluded: chain B residue 1609 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 51 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN B1556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.194454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.171923 restraints weight = 7770.030| |-----------------------------------------------------------------------------| r_work (start): 0.4826 rms_B_bonded: 2.25 r_work: 0.4640 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.130 5077 Z= 0.659 Angle : 1.143 13.038 6963 Z= 0.612 Chirality : 0.059 0.375 927 Planarity : 0.009 0.127 925 Dihedral : 8.992 30.471 826 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.39 % Allowed : 24.23 % Favored : 75.39 % Rotamer: Outliers : 9.54 % Allowed : 25.66 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.88 (0.23), residues: 776 helix: -1.88 (0.44), residues: 103 sheet: -4.19 (0.46), residues: 69 loop : -4.70 (0.19), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 499 HIS 0.011 0.003 HIS B1113 PHE 0.070 0.006 PHE B 634 TYR 0.024 0.004 TYR B 834 ARG 0.010 0.002 ARG B1586 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 22 time to evaluate : 0.500 Fit side-chains REVERT: B 228 GLN cc_start: 0.5437 (OUTLIER) cc_final: 0.4986 (tt0) REVERT: B 1156 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7338 (m-80) outliers start: 29 outliers final: 18 residues processed: 48 average time/residue: 0.0919 time to fit residues: 7.1283 Evaluate side-chains 42 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 22 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 634 PHE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1059 ASN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1150 SER Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain B residue 1226 SER Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1609 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 35 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 82 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 13 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5189 r_free = 0.5189 target = 0.212930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.187304 restraints weight = 7494.200| |-----------------------------------------------------------------------------| r_work (start): 0.4962 rms_B_bonded: 2.45 r_work: 0.4817 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5077 Z= 0.205 Angle : 0.718 9.955 6963 Z= 0.387 Chirality : 0.046 0.175 927 Planarity : 0.004 0.060 925 Dihedral : 6.883 27.873 826 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.66 % Favored : 86.34 % Rotamer: Outliers : 7.24 % Allowed : 28.95 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.22 (0.25), residues: 776 helix: -1.05 (0.49), residues: 103 sheet: -3.32 (0.58), residues: 57 loop : -4.35 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 499 HIS 0.006 0.001 HIS B 560 PHE 0.021 0.002 PHE B 634 TYR 0.012 0.002 TYR B 834 ARG 0.004 0.001 ARG B1586 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 22 time to evaluate : 0.549 Fit side-chains REVERT: B 228 GLN cc_start: 0.5016 (OUTLIER) cc_final: 0.4641 (tt0) REVERT: B 1062 GLU cc_start: 0.5734 (OUTLIER) cc_final: 0.5408 (tm-30) outliers start: 22 outliers final: 16 residues processed: 44 average time/residue: 0.0989 time to fit residues: 7.1047 Evaluate side-chains 40 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 22 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 966 THR Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1168 LYS Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1541 LEU Chi-restraints excluded: chain B residue 1609 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 53 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 0.0470 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 27 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 0.0000 chunk 73 optimal weight: 1.9990 overall best weight: 0.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5177 r_free = 0.5177 target = 0.209225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.184239 restraints weight = 7549.588| |-----------------------------------------------------------------------------| r_work (start): 0.4948 rms_B_bonded: 2.45 r_work: 0.4785 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5792 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5077 Z= 0.160 Angle : 0.638 11.364 6963 Z= 0.336 Chirality : 0.043 0.154 927 Planarity : 0.004 0.054 925 Dihedral : 5.804 22.614 826 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer: Outliers : 5.92 % Allowed : 31.25 % Favored : 62.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.26), residues: 776 helix: -0.23 (0.52), residues: 102 sheet: -3.12 (0.53), residues: 68 loop : -4.20 (0.20), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 499 HIS 0.005 0.001 HIS B 560 PHE 0.016 0.001 PHE B 634 TYR 0.007 0.001 TYR B 834 ARG 0.003 0.001 ARG B1075 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 26 time to evaluate : 0.577 Fit side-chains REVERT: B 228 GLN cc_start: 0.4828 (OUTLIER) cc_final: 0.4377 (tt0) outliers start: 18 outliers final: 13 residues processed: 43 average time/residue: 0.1020 time to fit residues: 7.2156 Evaluate side-chains 36 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 22 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1059 ASN Chi-restraints excluded: chain B residue 1086 HIS Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1541 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 59 optimal weight: 0.3980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5033 r_free = 0.5033 target = 0.194766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.172695 restraints weight = 7827.495| |-----------------------------------------------------------------------------| r_work (start): 0.4814 rms_B_bonded: 2.30 r_work: 0.4616 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 5077 Z= 0.424 Angle : 0.926 10.447 6963 Z= 0.492 Chirality : 0.052 0.286 927 Planarity : 0.007 0.110 925 Dihedral : 7.831 27.506 826 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.91 % Favored : 78.09 % Rotamer: Outliers : 6.25 % Allowed : 30.92 % Favored : 62.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.39 (0.25), residues: 776 helix: -1.04 (0.49), residues: 103 sheet: -3.86 (0.47), residues: 70 loop : -4.44 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 499 HIS 0.007 0.002 HIS B1115 PHE 0.058 0.005 PHE B 634 TYR 0.016 0.002 TYR B 834 ARG 0.008 0.001 ARG B1586 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 23 time to evaluate : 0.501 Fit side-chains REVERT: B 228 GLN cc_start: 0.5278 (OUTLIER) cc_final: 0.4801 (tt0) outliers start: 19 outliers final: 14 residues processed: 40 average time/residue: 0.0790 time to fit residues: 5.5980 Evaluate side-chains 38 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 23 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 966 THR Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1059 ASN Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1609 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 0.0270 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5084 r_free = 0.5084 target = 0.200002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.177523 restraints weight = 7812.242| |-----------------------------------------------------------------------------| r_work (start): 0.4871 rms_B_bonded: 2.45 r_work: 0.4693 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5077 Z= 0.241 Angle : 0.755 9.937 6963 Z= 0.402 Chirality : 0.046 0.173 927 Planarity : 0.005 0.056 925 Dihedral : 6.989 24.694 826 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.49 % Favored : 83.51 % Rotamer: Outliers : 4.28 % Allowed : 32.57 % Favored : 63.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.17 (0.25), residues: 776 helix: -0.82 (0.50), residues: 103 sheet: -3.31 (0.56), residues: 58 loop : -4.36 (0.20), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 499 HIS 0.006 0.001 HIS B1115 PHE 0.033 0.003 PHE B 634 TYR 0.011 0.002 TYR B1022 ARG 0.004 0.001 ARG B1586 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3198.63 seconds wall clock time: 57 minutes 9.80 seconds (3429.80 seconds total)