Starting phenix.real_space_refine on Sat Jun 21 21:28:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zgg_11205/06_2025/6zgg_11205.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zgg_11205/06_2025/6zgg_11205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zgg_11205/06_2025/6zgg_11205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zgg_11205/06_2025/6zgg_11205.map" model { file = "/net/cci-nas-00/data/ceres_data/6zgg_11205/06_2025/6zgg_11205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zgg_11205/06_2025/6zgg_11205.cif" } resolution = 3.8 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= 0.003 sd= 0.032 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 117 5.16 5 C 16014 2.51 5 N 4191 2.21 5 O 4774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 151 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25096 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8366 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 53, 'TRANS': 1015} Chain breaks: 5 Chain: "B" Number of atoms: 8380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8380 Classifications: {'peptide': 1071} Link IDs: {'PTRANS': 53, 'TRANS': 1017} Chain breaks: 5 Chain: "C" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8350 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 53, 'TRANS': 1013} Chain breaks: 5 Time building chain proxies: 16.15, per 1000 atoms: 0.64 Number of scatterers: 25096 At special positions: 0 Unit cell: (156.31, 149.842, 196.196, 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 117 16.00 O 4774 8.00 N 4191 7.00 C 16014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.60 Conformation dependent library (CDL) restraints added in 3.1 seconds 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6006 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 48 sheets defined 21.7% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.610A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.069A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 756 through 782 removed outlier: 3.954A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.553A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 948 Processing helix chain 'A' and resid 949 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 989 through 1033 Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.513A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.526A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.992A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.961A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.509A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 753 Processing helix chain 'B' and resid 756 through 782 removed outlier: 3.575A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.568A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 890' Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.920A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B 910 " --> pdb=" O PHE B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 938 removed outlier: 3.543A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 965 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.544A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 6.060A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.712A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 383 through 387 removed outlier: 4.169A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 756 through 782 removed outlier: 3.602A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.728A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 856 removed outlier: 3.525A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 949 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.614A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.746A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 3.907A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.868A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.821A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 11.181A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.445A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 9.193A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 310 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.651A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL A 395 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER A 514 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A 397 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL A 512 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER A 399 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 510 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL A 401 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR A 508 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.975A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.879A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A1075 " --> pdb=" O ILE A 712 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.913A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A1062 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.913A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A1062 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.246A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.522A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.648A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 51 removed outlier: 3.877A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 11.165A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 316 removed outlier: 5.947A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.547A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.924A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 664 through 665 removed outlier: 3.737A pdb=" N CYS B 671 " --> pdb=" O TYR B 695 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.737A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.715A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.715A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.404A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1076 through 1078 removed outlier: 3.905A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.769A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.745A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.385A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 152 through 160 removed outlier: 3.696A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 275 through 279 removed outlier: 4.234A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.596A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL C 395 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER C 514 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA C 397 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL C 512 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER C 399 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C 510 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL C 401 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR C 508 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 539 through 543 removed outlier: 5.911A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.082A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.504A pdb=" N PHE C1075 " --> pdb=" O ILE C 712 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 722 removed outlier: 3.727A pdb=" N THR C 719 " --> pdb=" O VAL C1068 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 722 removed outlier: 3.727A pdb=" N THR C 719 " --> pdb=" O VAL C1068 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 909 hydrogen bonds defined for protein. 2472 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: 11.37 Time building geometry restraints manager: 6.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8133 1.35 - 1.46: 6151 1.46 - 1.58: 11247 1.58 - 1.70: 0 1.70 - 1.82: 147 Bond restraints: 25678 Sorted by residual: bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.68e+00 bond pdb=" C MET A 177 " pdb=" O MET A 177 " ideal model delta sigma weight residual 1.227 1.235 -0.008 7.80e-03 1.64e+04 1.07e+00 bond pdb=" CA ASN B 211 " pdb=" C ASN B 211 " ideal model delta sigma weight residual 1.533 1.523 0.010 9.60e-03 1.09e+04 1.06e+00 bond pdb=" N PHE B 329 " pdb=" CA PHE B 329 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.41e-02 5.03e+03 1.02e+00 bond pdb=" CA ARG A 102 " pdb=" C ARG A 102 " ideal model delta sigma weight residual 1.517 1.523 -0.006 6.30e-03 2.52e+04 9.93e-01 ... (remaining 25673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 34566 1.68 - 3.35: 338 3.35 - 5.03: 28 5.03 - 6.71: 8 6.71 - 8.39: 1 Bond angle restraints: 34941 Sorted by residual: angle pdb=" CA ALA C 344 " pdb=" C ALA C 344 " pdb=" N THR C 345 " ideal model delta sigma weight residual 119.56 116.93 2.63 5.80e-01 2.97e+00 2.06e+01 angle pdb=" N ILE A 973 " pdb=" CA ILE A 973 " pdb=" C ILE A 973 " ideal model delta sigma weight residual 113.53 109.33 4.20 9.80e-01 1.04e+00 1.84e+01 angle pdb=" C MET A 177 " pdb=" CA MET A 177 " pdb=" CB MET A 177 " ideal model delta sigma weight residual 116.54 110.78 5.76 1.46e+00 4.69e-01 1.56e+01 angle pdb=" C ASP B 215 " pdb=" CA ASP B 215 " pdb=" CB ASP B 215 " ideal model delta sigma weight residual 115.89 110.76 5.13 1.32e+00 5.74e-01 1.51e+01 angle pdb=" C ASP C 215 " pdb=" CA ASP C 215 " pdb=" CB ASP C 215 " ideal model delta sigma weight residual 115.89 110.83 5.06 1.32e+00 5.74e-01 1.47e+01 ... (remaining 34936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 15035 17.59 - 35.18: 269 35.18 - 52.77: 15 52.77 - 70.36: 1 70.36 - 87.94: 3 Dihedral angle restraints: 15323 sinusoidal: 5987 harmonic: 9336 Sorted by residual: dihedral pdb=" N PHE B 329 " pdb=" C PHE B 329 " pdb=" CA PHE B 329 " pdb=" CB PHE B 329 " ideal model delta harmonic sigma weight residual 122.80 132.21 -9.41 0 2.50e+00 1.60e-01 1.42e+01 dihedral pdb=" C PHE B 329 " pdb=" N PHE B 329 " pdb=" CA PHE B 329 " pdb=" CB PHE B 329 " ideal model delta harmonic sigma weight residual -122.60 -131.02 8.42 0 2.50e+00 1.60e-01 1.13e+01 dihedral pdb=" SG CYS C 391 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " pdb=" CA CYS C 525 " ideal model delta sinusoidal sigma weight residual -73.00 -20.00 -53.00 1 2.00e+01 2.50e-03 9.56e+00 ... (remaining 15320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3576 0.069 - 0.138: 376 0.138 - 0.207: 0 0.207 - 0.276: 0 0.276 - 0.345: 1 Chirality restraints: 3953 Sorted by residual: chirality pdb=" CA PHE B 329 " pdb=" N PHE B 329 " pdb=" C PHE B 329 " pdb=" CB PHE B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA ILE C 664 " pdb=" N ILE C 664 " pdb=" C ILE C 664 " pdb=" CB ILE C 664 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE A 664 " pdb=" N ILE A 664 " pdb=" C ILE A 664 " pdb=" CB ILE A 664 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 3950 not shown) Planarity restraints: 4539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " 0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 986 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 985 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO B 986 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 986 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 986 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO C 986 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " -0.018 5.00e-02 4.00e+02 ... (remaining 4536 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3633 2.76 - 3.30: 22256 3.30 - 3.83: 39472 3.83 - 4.37: 43811 4.37 - 4.90: 79501 Nonbonded interactions: 188673 Sorted by model distance: nonbonded pdb=" O VAL A 130 " pdb=" OG1 THR A 167 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLU C1031 " pdb=" NH1 ARG C1039 " model vdw 2.297 3.120 nonbonded pdb=" OG1 THR C1076 " pdb=" OG SER C1097 " model vdw 2.305 3.040 nonbonded pdb=" OE2 GLU A1031 " pdb=" NH2 ARG C1039 " model vdw 2.305 3.120 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.306 3.040 ... (remaining 188668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 827 or resid 851 through 1146)) selection = (chain 'B' and (resid 14 through 617 or resid 641 through 827 or resid 851 throu \ gh 1146)) selection = chain 'C' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 60.260 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 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 : 0.001 0.030 25720 Z= 0.087 Angle : 0.414 8.387 35025 Z= 0.244 Chirality : 0.039 0.345 3953 Planarity : 0.003 0.034 4539 Dihedral : 5.801 87.945 9191 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.50 % Allowed : 12.36 % Favored : 87.13 % Rotamer: Outliers : 1.00 % Allowed : 3.07 % Favored : 95.94 % 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: -2.52 (0.14), residues: 3171 helix: 1.00 (0.21), residues: 607 sheet: -0.84 (0.20), residues: 626 loop : -3.06 (0.12), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 436 HIS 0.001 0.000 HIS B1048 PHE 0.006 0.000 PHE A 157 TYR 0.009 0.000 TYR B 204 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.13877 ( 861) hydrogen bonds : angle 5.55560 ( 2472) SS BOND : bond 0.00084 ( 42) SS BOND : angle 0.34151 ( 84) covalent geometry : bond 0.00140 (25678) covalent geometry : angle 0.41383 (34941) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 474 time to evaluate : 2.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 CYS cc_start: 0.5858 (OUTLIER) cc_final: 0.4332 (t) REVERT: A 206 LYS cc_start: 0.6346 (OUTLIER) cc_final: 0.5831 (mmmm) REVERT: A 300 LYS cc_start: 0.8576 (mttm) cc_final: 0.8358 (mtpp) REVERT: A 402 ILE cc_start: 0.8658 (pt) cc_final: 0.8145 (pt) REVERT: A 734 THR cc_start: 0.8611 (p) cc_final: 0.8390 (p) REVERT: A 968 SER cc_start: 0.9027 (m) cc_final: 0.8725 (t) REVERT: B 117 LEU cc_start: 0.9647 (tp) cc_final: 0.9108 (mp) REVERT: B 200 TYR cc_start: 0.9002 (m-80) cc_final: 0.8602 (m-80) REVERT: B 301 CYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7400 (m) REVERT: B 970 PHE cc_start: 0.8277 (m-10) cc_final: 0.7790 (m-10) REVERT: C 40 ASP cc_start: 0.8300 (p0) cc_final: 0.7840 (p0) REVERT: C 42 VAL cc_start: 0.8697 (t) cc_final: 0.8220 (p) REVERT: C 198 ASP cc_start: 0.7963 (m-30) cc_final: 0.7665 (m-30) REVERT: C 354 ASN cc_start: 0.8565 (t0) cc_final: 0.8135 (p0) REVERT: C 460 ASN cc_start: 0.8753 (m-40) cc_final: 0.7873 (t0) REVERT: C 855 PHE cc_start: 0.7480 (m-10) cc_final: 0.7230 (m-80) REVERT: C 1030 SER cc_start: 0.7658 (m) cc_final: 0.7181 (p) outliers start: 28 outliers final: 3 residues processed: 498 average time/residue: 0.4145 time to fit residues: 318.4438 Evaluate side-chains 249 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 243 time to evaluate : 4.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 210 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 5.9990 chunk 241 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 250 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 152 optimal weight: 20.0000 chunk 186 optimal weight: 5.9990 chunk 289 optimal weight: 4.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 17 ASN ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 134 GLN A 149 ASN A 173 GLN A 185 ASN A 211 ASN A 321 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 613 GLN A 675 GLN A 690 GLN A 787 GLN A 907 ASN A 920 GLN A 935 GLN A1005 GLN A1036 GLN A1054 GLN A1064 HIS A1098 ASN A1106 GLN A1125 ASN A1142 GLN B 14 GLN B 52 GLN B 61 ASN B 69 HIS B 115 GLN B 211 ASN B 218 GLN B 239 GLN B 245 HIS B 271 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 414 GLN B 540 ASN B 613 GLN B 690 GLN B 787 GLN B 920 GLN B 925 ASN B 935 GLN B 954 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN B1064 HIS B1071 GLN B1106 GLN C 14 GLN C 17 ASN C 23 GLN C 52 GLN C 61 ASN C 115 GLN C 146 HIS C 218 GLN C 271 GLN C 314 GLN C 370 ASN C 422 ASN C 519 HIS C 536 ASN C 613 GLN C 675 GLN C 710 ASN C 764 ASN C 784 GLN C 853 GLN C 907 ASN C 920 GLN C 935 GLN C 954 GLN C1005 GLN C1011 GLN C1054 GLN C1058 HIS ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.085998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.056666 restraints weight = 113105.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.058720 restraints weight = 54835.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.060017 restraints weight = 34137.200| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.200 25720 Z= 0.324 Angle : 0.787 12.882 35025 Z= 0.409 Chirality : 0.047 0.252 3953 Planarity : 0.005 0.127 4539 Dihedral : 4.278 57.391 3451 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.84 % Favored : 93.13 % Rotamer: Outliers : 2.92 % Allowed : 8.88 % Favored : 88.20 % 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: -1.85 (0.14), residues: 3171 helix: 1.10 (0.21), residues: 643 sheet: -0.32 (0.20), residues: 693 loop : -2.63 (0.12), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 104 HIS 0.011 0.002 HIS C 66 PHE 0.034 0.002 PHE C 782 TYR 0.032 0.002 TYR C 396 ARG 0.010 0.001 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.06111 ( 861) hydrogen bonds : angle 4.91649 ( 2472) SS BOND : bond 0.01018 ( 42) SS BOND : angle 1.18050 ( 84) covalent geometry : bond 0.00732 (25678) covalent geometry : angle 0.78539 (34941) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 190 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8321 (mtt-85) cc_final: 0.7935 (mtp85) REVERT: A 206 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6368 (mmmm) REVERT: A 270 LEU cc_start: 0.9387 (mp) cc_final: 0.9135 (mp) REVERT: A 402 ILE cc_start: 0.8346 (pt) cc_final: 0.8015 (pt) REVERT: A 964 LYS cc_start: 0.9473 (OUTLIER) cc_final: 0.8992 (ttpp) REVERT: A 994 ASP cc_start: 0.7512 (t0) cc_final: 0.7311 (t70) REVERT: B 118 LEU cc_start: 0.8896 (tp) cc_final: 0.8530 (mp) REVERT: B 200 TYR cc_start: 0.9327 (m-80) cc_final: 0.8801 (m-80) REVERT: B 269 TYR cc_start: 0.7957 (m-80) cc_final: 0.7621 (m-80) REVERT: B 1017 GLU cc_start: 0.8404 (tp30) cc_final: 0.8147 (tp30) REVERT: C 40 ASP cc_start: 0.8641 (p0) cc_final: 0.8353 (p0) REVERT: C 141 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8906 (tt) REVERT: C 238 PHE cc_start: 0.8337 (p90) cc_final: 0.7527 (p90) REVERT: C 338 PHE cc_start: 0.8485 (m-10) cc_final: 0.8262 (m-10) REVERT: C 354 ASN cc_start: 0.8744 (t0) cc_final: 0.8078 (p0) REVERT: C 386 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8385 (mtpp) REVERT: C 460 ASN cc_start: 0.9152 (m-40) cc_final: 0.8283 (t0) REVERT: C 773 GLU cc_start: 0.8563 (tp30) cc_final: 0.8034 (tm-30) REVERT: C 984 LEU cc_start: 0.8072 (mm) cc_final: 0.7310 (tp) REVERT: C 1107 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7772 (mtt180) outliers start: 82 outliers final: 48 residues processed: 254 average time/residue: 0.4684 time to fit residues: 191.3768 Evaluate side-chains 188 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 136 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 286 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 chunk 227 optimal weight: 6.9990 chunk 197 optimal weight: 0.5980 chunk 183 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 247 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B1083 HIS C 331 ASN C 907 ASN C1064 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.087039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.059338 restraints weight = 108529.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.061807 restraints weight = 54484.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.062608 restraints weight = 29471.066| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 25720 Z= 0.151 Angle : 0.545 11.635 35025 Z= 0.276 Chirality : 0.042 0.152 3953 Planarity : 0.004 0.046 4539 Dihedral : 3.731 59.872 3446 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % Rotamer: Outliers : 2.82 % Allowed : 9.80 % Favored : 87.38 % 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: -1.36 (0.15), residues: 3171 helix: 1.85 (0.22), residues: 632 sheet: -0.00 (0.21), residues: 643 loop : -2.36 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 104 HIS 0.005 0.001 HIS A 49 PHE 0.015 0.001 PHE C 782 TYR 0.023 0.001 TYR C 396 ARG 0.004 0.000 ARG C 509 Details of bonding type rmsd hydrogen bonds : bond 0.04808 ( 861) hydrogen bonds : angle 4.32839 ( 2472) SS BOND : bond 0.00358 ( 42) SS BOND : angle 0.96917 ( 84) covalent geometry : bond 0.00344 (25678) covalent geometry : angle 0.54362 (34941) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 148 time to evaluate : 3.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.9386 (mp) cc_final: 0.9094 (mp) REVERT: A 964 LYS cc_start: 0.9511 (OUTLIER) cc_final: 0.9146 (ttpp) REVERT: B 118 LEU cc_start: 0.8748 (tp) cc_final: 0.8478 (mp) REVERT: B 141 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8375 (tt) REVERT: B 200 TYR cc_start: 0.9324 (m-80) cc_final: 0.8788 (m-80) REVERT: B 223 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7836 (mm) REVERT: B 228 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8426 (t0) REVERT: B 301 CYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7606 (m) REVERT: B 592 PHE cc_start: 0.3880 (OUTLIER) cc_final: 0.3590 (m-80) REVERT: B 984 LEU cc_start: 0.8883 (tp) cc_final: 0.8555 (tt) REVERT: C 40 ASP cc_start: 0.8591 (p0) cc_final: 0.8347 (p0) REVERT: C 141 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8818 (tt) REVERT: C 238 PHE cc_start: 0.8422 (p90) cc_final: 0.7593 (p90) REVERT: C 242 LEU cc_start: 0.8772 (mm) cc_final: 0.8255 (tp) REVERT: C 386 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8406 (mtpp) REVERT: C 456 PHE cc_start: 0.7821 (t80) cc_final: 0.7395 (t80) REVERT: C 460 ASN cc_start: 0.9170 (m-40) cc_final: 0.8425 (t0) REVERT: C 855 PHE cc_start: 0.7989 (m-10) cc_final: 0.7724 (m-80) REVERT: C 984 LEU cc_start: 0.8022 (mm) cc_final: 0.7256 (tp) REVERT: C 1107 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7970 (mtt180) outliers start: 79 outliers final: 49 residues processed: 215 average time/residue: 0.3613 time to fit residues: 128.1677 Evaluate side-chains 185 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 128 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 254 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 290 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 250 optimal weight: 9.9990 chunk 297 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 313 optimal weight: 3.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 66 HIS A 188 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN B 69 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1074 ASN C 66 HIS C 895 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.085490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.057957 restraints weight = 112130.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.059885 restraints weight = 53428.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.060223 restraints weight = 29732.542| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 25720 Z= 0.154 Angle : 0.530 11.252 35025 Z= 0.269 Chirality : 0.041 0.148 3953 Planarity : 0.004 0.049 4539 Dihedral : 3.805 59.026 3446 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.11 % Favored : 94.86 % Rotamer: Outliers : 3.03 % Allowed : 9.45 % Favored : 87.52 % 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: -1.10 (0.15), residues: 3171 helix: 1.96 (0.21), residues: 636 sheet: 0.17 (0.20), residues: 683 loop : -2.22 (0.13), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 436 HIS 0.006 0.001 HIS C1064 PHE 0.022 0.001 PHE B 55 TYR 0.018 0.001 TYR C 396 ARG 0.004 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.04777 ( 861) hydrogen bonds : angle 4.24951 ( 2472) SS BOND : bond 0.00185 ( 42) SS BOND : angle 0.79126 ( 84) covalent geometry : bond 0.00354 (25678) covalent geometry : angle 0.52914 (34941) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 130 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.4495 (OUTLIER) cc_final: 0.4172 (pp30) REVERT: A 270 LEU cc_start: 0.9373 (mp) cc_final: 0.9080 (mp) REVERT: A 964 LYS cc_start: 0.9480 (OUTLIER) cc_final: 0.9163 (ttpp) REVERT: B 135 PHE cc_start: 0.7495 (m-80) cc_final: 0.6967 (m-80) REVERT: B 141 LEU cc_start: 0.9286 (mt) cc_final: 0.8322 (tt) REVERT: B 200 TYR cc_start: 0.9326 (m-80) cc_final: 0.8780 (m-80) REVERT: B 223 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7870 (mm) REVERT: B 1028 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8751 (ttmt) REVERT: C 141 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8730 (tt) REVERT: C 238 PHE cc_start: 0.8461 (p90) cc_final: 0.7683 (p90) REVERT: C 242 LEU cc_start: 0.8737 (mm) cc_final: 0.8195 (tp) REVERT: C 338 PHE cc_start: 0.8637 (m-10) cc_final: 0.8355 (m-10) REVERT: C 456 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7428 (t80) REVERT: C 460 ASN cc_start: 0.9206 (m-40) cc_final: 0.8299 (t0) REVERT: C 740 MET cc_start: 0.8919 (tmm) cc_final: 0.8671 (tmm) REVERT: C 1107 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7949 (mtt180) outliers start: 85 outliers final: 53 residues processed: 204 average time/residue: 0.4786 time to fit residues: 162.2952 Evaluate side-chains 177 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 117 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 226 optimal weight: 6.9990 chunk 269 optimal weight: 0.7980 chunk 316 optimal weight: 4.9990 chunk 294 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 280 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 207 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN B 66 HIS B 69 HIS B 360 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.082528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.053562 restraints weight = 112175.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.055971 restraints weight = 55892.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.057413 restraints weight = 28584.589| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 25720 Z= 0.213 Angle : 0.588 13.664 35025 Z= 0.298 Chirality : 0.042 0.148 3953 Planarity : 0.004 0.053 4539 Dihedral : 3.917 48.571 3445 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.90 % Favored : 94.07 % Rotamer: Outliers : 3.24 % Allowed : 10.12 % Favored : 86.63 % 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: -1.07 (0.15), residues: 3171 helix: 1.79 (0.21), residues: 634 sheet: 0.15 (0.20), residues: 691 loop : -2.10 (0.13), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 436 HIS 0.007 0.001 HIS A1064 PHE 0.024 0.001 PHE C 562 TYR 0.021 0.001 TYR B 505 ARG 0.012 0.000 ARG B 403 Details of bonding type rmsd hydrogen bonds : bond 0.05457 ( 861) hydrogen bonds : angle 4.48685 ( 2472) SS BOND : bond 0.00482 ( 42) SS BOND : angle 0.80715 ( 84) covalent geometry : bond 0.00489 (25678) covalent geometry : angle 0.58743 (34941) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 113 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.5061 (OUTLIER) cc_final: 0.4839 (pp30) REVERT: A 270 LEU cc_start: 0.9396 (mp) cc_final: 0.9102 (mp) REVERT: A 964 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9133 (ttpp) REVERT: B 141 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8457 (tt) REVERT: B 200 TYR cc_start: 0.9411 (m-80) cc_final: 0.8793 (m-80) REVERT: B 223 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8074 (mm) REVERT: C 141 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8855 (tt) REVERT: C 238 PHE cc_start: 0.8514 (p90) cc_final: 0.7658 (p90) REVERT: C 242 LEU cc_start: 0.8909 (mm) cc_final: 0.8309 (tp) REVERT: C 338 PHE cc_start: 0.8952 (m-10) cc_final: 0.8749 (m-10) REVERT: C 456 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7636 (t80) REVERT: C 460 ASN cc_start: 0.9288 (m-40) cc_final: 0.8315 (t0) REVERT: C 740 MET cc_start: 0.8949 (tmm) cc_final: 0.8638 (tmm) REVERT: C 855 PHE cc_start: 0.8196 (m-10) cc_final: 0.7845 (m-80) REVERT: C 1107 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7922 (mtt180) outliers start: 91 outliers final: 64 residues processed: 193 average time/residue: 0.4038 time to fit residues: 131.8474 Evaluate side-chains 171 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 100 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 107 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 277 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 289 optimal weight: 3.9990 chunk 224 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 260 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS B 125 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.080266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.051517 restraints weight = 112916.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.053560 restraints weight = 59607.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.053911 restraints weight = 31997.491| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.6128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.134 25720 Z= 0.299 Angle : 0.687 11.209 35025 Z= 0.352 Chirality : 0.045 0.303 3953 Planarity : 0.004 0.051 4539 Dihedral : 4.484 48.951 3445 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.28 % Favored : 93.69 % Rotamer: Outliers : 3.53 % Allowed : 10.84 % Favored : 85.63 % 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: -1.32 (0.14), residues: 3171 helix: 1.27 (0.21), residues: 632 sheet: -0.03 (0.19), residues: 724 loop : -2.15 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 353 HIS 0.009 0.002 HIS A1064 PHE 0.023 0.002 PHE C 782 TYR 0.020 0.002 TYR C 396 ARG 0.005 0.001 ARG B1091 Details of bonding type rmsd hydrogen bonds : bond 0.06492 ( 861) hydrogen bonds : angle 4.99167 ( 2472) SS BOND : bond 0.00302 ( 42) SS BOND : angle 0.97043 ( 84) covalent geometry : bond 0.00685 (25678) covalent geometry : angle 0.68590 (34941) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 100 time to evaluate : 4.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.9418 (mp) cc_final: 0.9179 (mp) REVERT: A 872 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8964 (tm-30) REVERT: A 964 LYS cc_start: 0.9464 (OUTLIER) cc_final: 0.9111 (ttpp) REVERT: B 141 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8361 (tt) REVERT: B 200 TYR cc_start: 0.9514 (m-80) cc_final: 0.8829 (m-80) REVERT: C 238 PHE cc_start: 0.8571 (p90) cc_final: 0.7668 (p90) REVERT: C 456 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7824 (t80) REVERT: C 740 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8688 (tmm) REVERT: C 756 TYR cc_start: 0.5828 (OUTLIER) cc_final: 0.5446 (m-80) REVERT: C 1107 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8145 (mtt180) outliers start: 99 outliers final: 71 residues processed: 184 average time/residue: 0.4470 time to fit residues: 141.3487 Evaluate side-chains 169 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 91 time to evaluate : 4.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 80 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 190 optimal weight: 0.5980 chunk 168 optimal weight: 0.7980 chunk 231 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 282 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 394 ASN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 957 GLN C 121 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.082329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.053288 restraints weight = 111678.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.055311 restraints weight = 52623.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.056591 restraints weight = 32414.606| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25720 Z= 0.114 Angle : 0.514 14.236 35025 Z= 0.257 Chirality : 0.042 0.155 3953 Planarity : 0.004 0.051 4539 Dihedral : 3.880 47.859 3445 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 2.10 % Allowed : 12.37 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.89 (0.15), residues: 3171 helix: 2.05 (0.21), residues: 622 sheet: 0.24 (0.20), residues: 689 loop : -1.98 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 152 HIS 0.002 0.001 HIS B1048 PHE 0.020 0.001 PHE C 186 TYR 0.016 0.001 TYR C 756 ARG 0.003 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.04890 ( 861) hydrogen bonds : angle 4.31698 ( 2472) SS BOND : bond 0.00250 ( 42) SS BOND : angle 0.76709 ( 84) covalent geometry : bond 0.00242 (25678) covalent geometry : angle 0.51359 (34941) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 106 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.5092 (OUTLIER) cc_final: 0.4845 (pp30) REVERT: A 223 LEU cc_start: 0.8629 (mt) cc_final: 0.8014 (tp) REVERT: A 270 LEU cc_start: 0.9426 (mp) cc_final: 0.9209 (mp) REVERT: A 964 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9071 (ttpp) REVERT: B 141 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8307 (tt) REVERT: B 200 TYR cc_start: 0.9348 (m-80) cc_final: 0.8640 (m-80) REVERT: C 238 PHE cc_start: 0.8602 (p90) cc_final: 0.7778 (p90) REVERT: C 242 LEU cc_start: 0.8965 (mm) cc_final: 0.8428 (tp) REVERT: C 456 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7588 (t80) REVERT: C 740 MET cc_start: 0.8952 (tmm) cc_final: 0.8659 (tmm) REVERT: C 1107 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8288 (mtt90) outliers start: 59 outliers final: 42 residues processed: 153 average time/residue: 0.3322 time to fit residues: 87.1529 Evaluate side-chains 143 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 96 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 55 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 301 optimal weight: 0.8980 chunk 311 optimal weight: 1.9990 chunk 144 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 247 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.081510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.052339 restraints weight = 112590.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054281 restraints weight = 53553.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.055517 restraints weight = 33342.761| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.6180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 25720 Z= 0.163 Angle : 0.542 13.054 35025 Z= 0.272 Chirality : 0.042 0.157 3953 Planarity : 0.004 0.051 4539 Dihedral : 3.911 47.361 3445 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.92 % Favored : 95.05 % Rotamer: Outliers : 2.14 % Allowed : 12.69 % Favored : 85.17 % 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: -0.88 (0.15), residues: 3171 helix: 1.92 (0.21), residues: 632 sheet: 0.18 (0.20), residues: 688 loop : -1.91 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 152 HIS 0.005 0.001 HIS C1064 PHE 0.015 0.001 PHE C 55 TYR 0.015 0.001 TYR C 756 ARG 0.008 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.05116 ( 861) hydrogen bonds : angle 4.38109 ( 2472) SS BOND : bond 0.00278 ( 42) SS BOND : angle 0.87783 ( 84) covalent geometry : bond 0.00372 (25678) covalent geometry : angle 0.54069 (34941) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 99 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8705 (mt) cc_final: 0.8011 (tp) REVERT: A 270 LEU cc_start: 0.9443 (mp) cc_final: 0.9235 (mp) REVERT: A 964 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.9110 (ttpp) REVERT: B 141 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8330 (tt) REVERT: B 200 TYR cc_start: 0.9449 (m-80) cc_final: 0.8718 (m-80) REVERT: C 238 PHE cc_start: 0.8600 (p90) cc_final: 0.7714 (p90) REVERT: C 242 LEU cc_start: 0.8983 (mm) cc_final: 0.8402 (tp) REVERT: C 338 PHE cc_start: 0.8874 (m-10) cc_final: 0.8568 (m-10) REVERT: C 456 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7670 (t80) REVERT: C 740 MET cc_start: 0.9003 (tmm) cc_final: 0.8692 (tmm) REVERT: C 1107 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7979 (mtt180) outliers start: 60 outliers final: 47 residues processed: 147 average time/residue: 0.3165 time to fit residues: 80.3184 Evaluate side-chains 148 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 97 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 9 optimal weight: 9.9990 chunk 308 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 119 optimal weight: 0.0050 chunk 148 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.080926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.051636 restraints weight = 113331.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.053568 restraints weight = 54160.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.054779 restraints weight = 33594.275| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 25720 Z= 0.176 Angle : 0.559 12.920 35025 Z= 0.283 Chirality : 0.042 0.151 3953 Planarity : 0.004 0.052 4539 Dihedral : 4.012 46.931 3445 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.11 % Favored : 94.86 % Rotamer: Outliers : 2.17 % Allowed : 12.73 % Favored : 85.10 % 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: -0.86 (0.15), residues: 3171 helix: 1.80 (0.21), residues: 644 sheet: 0.20 (0.19), residues: 711 loop : -1.89 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 353 HIS 0.005 0.001 HIS A1064 PHE 0.014 0.001 PHE C 186 TYR 0.017 0.001 TYR C 756 ARG 0.005 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.05359 ( 861) hydrogen bonds : angle 4.47185 ( 2472) SS BOND : bond 0.00220 ( 42) SS BOND : angle 0.89793 ( 84) covalent geometry : bond 0.00406 (25678) covalent geometry : angle 0.55789 (34941) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 98 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8757 (mt) cc_final: 0.8095 (tp) REVERT: A 270 LEU cc_start: 0.9439 (mp) cc_final: 0.9236 (mp) REVERT: A 964 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.9107 (ttpp) REVERT: B 141 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8305 (tt) REVERT: B 200 TYR cc_start: 0.9460 (m-80) cc_final: 0.8732 (m-80) REVERT: B 753 LEU cc_start: 0.9296 (tp) cc_final: 0.9064 (tt) REVERT: C 238 PHE cc_start: 0.8570 (p90) cc_final: 0.7656 (p90) REVERT: C 242 LEU cc_start: 0.9009 (mm) cc_final: 0.8439 (tp) REVERT: C 456 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7740 (t80) REVERT: C 740 MET cc_start: 0.9015 (tmm) cc_final: 0.8659 (tmm) REVERT: C 1107 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8322 (mtt90) outliers start: 61 outliers final: 53 residues processed: 150 average time/residue: 0.3137 time to fit residues: 82.1658 Evaluate side-chains 150 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 93 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 158 optimal weight: 7.9990 chunk 193 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 43 optimal weight: 8.9990 chunk 146 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 95 optimal weight: 0.4980 chunk 216 optimal weight: 0.5980 chunk 303 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.082514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.053939 restraints weight = 111262.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.056532 restraints weight = 54524.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.057601 restraints weight = 28214.960| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25720 Z= 0.093 Angle : 0.512 13.787 35025 Z= 0.253 Chirality : 0.042 0.158 3953 Planarity : 0.003 0.052 4539 Dihedral : 3.719 46.941 3445 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.97 % Favored : 95.99 % Rotamer: Outliers : 2.00 % Allowed : 13.12 % Favored : 84.88 % 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: -0.62 (0.15), residues: 3171 helix: 2.15 (0.21), residues: 638 sheet: 0.28 (0.20), residues: 697 loop : -1.74 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.003 0.001 HIS B1048 PHE 0.014 0.001 PHE B1121 TYR 0.045 0.001 TYR B 904 ARG 0.005 0.000 ARG A1107 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 861) hydrogen bonds : angle 4.10415 ( 2472) SS BOND : bond 0.00200 ( 42) SS BOND : angle 0.71524 ( 84) covalent geometry : bond 0.00200 (25678) covalent geometry : angle 0.51185 (34941) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 106 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8616 (mt) cc_final: 0.8121 (tp) REVERT: A 270 LEU cc_start: 0.9426 (mp) cc_final: 0.9197 (mp) REVERT: A 964 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9097 (ttpp) REVERT: B 141 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8211 (tt) REVERT: B 200 TYR cc_start: 0.9372 (m-80) cc_final: 0.8667 (m-80) REVERT: C 177 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7452 (pmm) REVERT: C 238 PHE cc_start: 0.8556 (p90) cc_final: 0.7653 (p90) REVERT: C 242 LEU cc_start: 0.9046 (mm) cc_final: 0.8532 (tp) REVERT: C 338 PHE cc_start: 0.8996 (m-10) cc_final: 0.8710 (m-10) REVERT: C 456 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7742 (t80) REVERT: C 740 MET cc_start: 0.9028 (tmm) cc_final: 0.8670 (tmm) REVERT: C 1107 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8270 (mtt90) outliers start: 56 outliers final: 42 residues processed: 152 average time/residue: 0.3712 time to fit residues: 96.9204 Evaluate side-chains 145 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 98 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 58 optimal weight: 0.0570 chunk 138 optimal weight: 0.0670 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 178 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.082706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.054327 restraints weight = 112040.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.056974 restraints weight = 54640.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.058306 restraints weight = 27826.700| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.6344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25720 Z= 0.094 Angle : 0.504 13.207 35025 Z= 0.248 Chirality : 0.041 0.149 3953 Planarity : 0.003 0.053 4539 Dihedral : 3.570 47.413 3445 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.77 % Rotamer: Outliers : 1.71 % Allowed : 13.44 % Favored : 84.85 % 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: -0.46 (0.15), residues: 3171 helix: 2.25 (0.21), residues: 640 sheet: 0.42 (0.20), residues: 695 loop : -1.65 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.001 HIS A 207 PHE 0.014 0.001 PHE B1121 TYR 0.021 0.001 TYR B 904 ARG 0.005 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 861) hydrogen bonds : angle 4.02530 ( 2472) SS BOND : bond 0.00175 ( 42) SS BOND : angle 0.70214 ( 84) covalent geometry : bond 0.00206 (25678) covalent geometry : angle 0.50386 (34941) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9288.99 seconds wall clock time: 166 minutes 26.50 seconds (9986.50 seconds total)