Starting phenix.real_space_refine on Mon Aug 25 04:29:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zgg_11205/08_2025/6zgg_11205.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zgg_11205/08_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_11205/08_2025/6zgg_11205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zgg_11205/08_2025/6zgg_11205.map" model { file = "/net/cci-nas-00/data/ceres_data/6zgg_11205/08_2025/6zgg_11205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zgg_11205/08_2025/6zgg_11205.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.27, per 1000 atoms: 0.21 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: 1.71 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.01 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: 5.44 Time building geometry restraints manager: 2.36 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: 5.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.260 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.490 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.002 0.000 ARG A 357 TYR 0.009 0.000 TYR B 204 PHE 0.006 0.000 PHE A 157 TRP 0.004 0.000 TRP A 436 HIS 0.001 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00140 (25678) covalent geometry : angle 0.41383 (34941) SS BOND : bond 0.00084 ( 42) SS BOND : angle 0.34151 ( 84) hydrogen bonds : bond 0.13877 ( 861) hydrogen bonds : angle 5.55560 ( 2472) *********************** 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 : 0.784 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: symmetry clash revert: symmetry clash REVERT: A 166 CYS cc_start: 0.5858 (OUTLIER) cc_final: 0.4333 (t) REVERT: A 206 LYS cc_start: 0.6346 (OUTLIER) cc_final: 0.5829 (mmmm) REVERT: A 300 LYS cc_start: 0.8576 (mttm) cc_final: 0.8359 (mtpp) REVERT: A 402 ILE cc_start: 0.8658 (pt) cc_final: 0.8144 (pt) REVERT: A 734 THR cc_start: 0.8611 (p) cc_final: 0.8389 (p) REVERT: A 968 SER cc_start: 0.9027 (m) cc_final: 0.8724 (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: 0.7791 (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: 0.8133 (p0) REVERT: C 460 ASN cc_start: 0.8753 (m-40) cc_final: 0.7872 (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: 0.7176 (p) outliers start: 28 outliers final: 3 residues processed: 498 average time/residue: 0.1558 time to fit residues: 119.9608 Evaluate side-chains 244 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 238 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 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 52 GLN B 61 ASN B 69 HIS B 115 GLN B 211 ASN B 218 GLN B 239 GLN B 271 GLN B 282 ASN 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 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 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 C1064 HIS C1071 GLN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.088117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.060273 restraints weight = 112342.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.063146 restraints weight = 54689.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.063905 restraints weight = 28506.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.064446 restraints weight = 21722.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.064538 restraints weight = 20056.163| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.167 25720 Z= 0.276 Angle : 0.719 11.922 35025 Z= 0.370 Chirality : 0.045 0.317 3953 Planarity : 0.005 0.146 4539 Dihedral : 4.048 55.548 3451 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.99 % Favored : 93.98 % Rotamer: Outliers : 2.82 % Allowed : 8.56 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.14), residues: 3171 helix: 1.37 (0.21), residues: 642 sheet: -0.30 (0.20), residues: 689 loop : -2.62 (0.12), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 273 TYR 0.018 0.002 TYR B 756 PHE 0.033 0.002 PHE C 782 TRP 0.030 0.002 TRP C 104 HIS 0.009 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00638 (25678) covalent geometry : angle 0.71814 (34941) SS BOND : bond 0.00789 ( 42) SS BOND : angle 1.11932 ( 84) hydrogen bonds : bond 0.05278 ( 861) hydrogen bonds : angle 4.64192 ( 2472) *********************** 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 275 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 196 time to evaluate : 0.711 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 206 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6207 (mmmm) REVERT: A 270 LEU cc_start: 0.9373 (mp) cc_final: 0.9103 (mp) REVERT: A 402 ILE cc_start: 0.8224 (pt) cc_final: 0.7869 (pt) REVERT: A 964 LYS cc_start: 0.9464 (OUTLIER) cc_final: 0.9015 (ttpp) REVERT: A 994 ASP cc_start: 0.7316 (t0) cc_final: 0.7093 (t70) REVERT: B 118 LEU cc_start: 0.8868 (tp) cc_final: 0.8516 (mp) REVERT: B 200 TYR cc_start: 0.9273 (m-80) cc_final: 0.8760 (m-80) REVERT: B 269 TYR cc_start: 0.7924 (m-80) cc_final: 0.7616 (m-80) REVERT: B 301 CYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7775 (m) REVERT: B 1017 GLU cc_start: 0.8326 (tp30) cc_final: 0.8098 (tp30) REVERT: C 40 ASP cc_start: 0.8587 (p0) cc_final: 0.8311 (p0) REVERT: C 141 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8942 (tp) REVERT: C 238 PHE cc_start: 0.8323 (p90) cc_final: 0.7540 (p90) REVERT: C 338 PHE cc_start: 0.8391 (m-10) cc_final: 0.8169 (m-10) REVERT: C 354 ASN cc_start: 0.8766 (t0) cc_final: 0.8127 (p0) REVERT: C 386 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8326 (mtpp) REVERT: C 460 ASN cc_start: 0.9136 (m-40) cc_final: 0.8292 (t0) REVERT: C 773 GLU cc_start: 0.8512 (tp30) cc_final: 0.8049 (tm-30) REVERT: C 900 MET cc_start: 0.8726 (mtt) cc_final: 0.8518 (mtt) REVERT: C 959 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8421 (mt) REVERT: C 1107 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7892 (mtt180) outliers start: 79 outliers final: 45 residues processed: 257 average time/residue: 0.1430 time to fit residues: 58.8863 Evaluate side-chains 196 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP 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 736 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1094 VAL 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 296 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 595 VAL 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 938 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE 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 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 959 LEU 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 87 optimal weight: 0.7980 chunk 219 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 205 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 chunk 209 optimal weight: 0.6980 chunk 287 optimal weight: 0.7980 chunk 192 optimal weight: 0.7980 chunk 294 optimal weight: 0.7980 chunk 300 optimal weight: 0.9980 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN B 14 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1074 ASN C 331 ASN C 895 GLN C 907 ASN C1023 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.088816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.061948 restraints weight = 110686.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.064087 restraints weight = 52639.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.065090 restraints weight = 27759.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.065328 restraints weight = 24984.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.065308 restraints weight = 21761.620| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 25720 Z= 0.110 Angle : 0.513 12.948 35025 Z= 0.256 Chirality : 0.041 0.150 3953 Planarity : 0.003 0.043 4539 Dihedral : 3.467 55.838 3446 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer: Outliers : 2.17 % Allowed : 9.80 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.15), residues: 3171 helix: 2.08 (0.22), residues: 632 sheet: -0.02 (0.20), residues: 660 loop : -2.37 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 44 TYR 0.020 0.001 TYR A 495 PHE 0.013 0.001 PHE A 898 TRP 0.014 0.001 TRP C 104 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00249 (25678) covalent geometry : angle 0.51207 (34941) SS BOND : bond 0.00423 ( 42) SS BOND : angle 0.90841 ( 84) hydrogen bonds : bond 0.04044 ( 861) hydrogen bonds : angle 4.10285 ( 2472) *********************** 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 223 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 162 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9098 (mp) REVERT: A 270 LEU cc_start: 0.9364 (mp) cc_final: 0.9081 (mp) REVERT: A 786 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7875 (tppt) REVERT: A 964 LYS cc_start: 0.9493 (OUTLIER) cc_final: 0.9115 (ttpp) REVERT: B 117 LEU cc_start: 0.9504 (tt) cc_final: 0.8721 (mp) REVERT: B 118 LEU cc_start: 0.8744 (tp) cc_final: 0.8398 (mt) REVERT: B 141 LEU cc_start: 0.9335 (mt) cc_final: 0.8429 (tt) REVERT: B 200 TYR cc_start: 0.9266 (m-80) cc_final: 0.8702 (m-80) REVERT: B 223 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7851 (mm) REVERT: B 269 TYR cc_start: 0.7898 (m-80) cc_final: 0.7629 (m-80) REVERT: B 592 PHE cc_start: 0.3616 (OUTLIER) cc_final: 0.2893 (m-80) REVERT: B 979 ASP cc_start: 0.8841 (t0) cc_final: 0.8496 (t0) REVERT: B 1017 GLU cc_start: 0.8280 (tp30) cc_final: 0.8015 (tp30) REVERT: C 40 ASP cc_start: 0.8637 (p0) cc_final: 0.8374 (p0) REVERT: C 141 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8788 (tt) REVERT: C 238 PHE cc_start: 0.8349 (p90) cc_final: 0.7567 (p90) REVERT: C 242 LEU cc_start: 0.8848 (mm) cc_final: 0.8315 (tp) REVERT: C 338 PHE cc_start: 0.8298 (m-10) cc_final: 0.7985 (m-10) REVERT: C 354 ASN cc_start: 0.8753 (t0) cc_final: 0.8178 (p0) REVERT: C 386 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8225 (mtpp) REVERT: C 456 PHE cc_start: 0.7783 (t80) cc_final: 0.7396 (t80) REVERT: C 460 ASN cc_start: 0.9212 (m-40) cc_final: 0.8371 (t0) REVERT: C 773 GLU cc_start: 0.8474 (tp30) cc_final: 0.8221 (tm-30) REVERT: C 855 PHE cc_start: 0.7933 (m-10) cc_final: 0.7677 (m-80) REVERT: C 959 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8542 (mt) REVERT: C 984 LEU cc_start: 0.7936 (mm) cc_final: 0.7237 (tp) REVERT: C 1107 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7886 (mtt180) outliers start: 61 outliers final: 38 residues processed: 215 average time/residue: 0.1411 time to fit residues: 49.7436 Evaluate side-chains 180 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 135 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 206 LYS 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 538 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 938 LEU 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 47 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 592 PHE 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 938 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 PHE 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 345 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 959 LEU 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 88 optimal weight: 2.9990 chunk 226 optimal weight: 0.2980 chunk 117 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 284 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 49 HIS A 66 HIS A1108 ASN B 69 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 66 HIS C1058 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.085193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.057645 restraints weight = 111197.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.059420 restraints weight = 53892.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.059740 restraints weight = 31053.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.060041 restraints weight = 31767.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.060141 restraints weight = 27035.002| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 25720 Z= 0.199 Angle : 0.597 10.758 35025 Z= 0.303 Chirality : 0.042 0.152 3953 Planarity : 0.004 0.049 4539 Dihedral : 3.803 46.033 3445 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.55 % Favored : 94.42 % Rotamer: Outliers : 3.21 % Allowed : 9.23 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.15), residues: 3171 helix: 1.83 (0.21), residues: 625 sheet: 0.23 (0.20), residues: 667 loop : -2.22 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 983 TYR 0.016 0.001 TYR C 204 PHE 0.027 0.002 PHE C 782 TRP 0.023 0.002 TRP C 436 HIS 0.015 0.002 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00458 (25678) covalent geometry : angle 0.59590 (34941) SS BOND : bond 0.00577 ( 42) SS BOND : angle 0.86426 ( 84) hydrogen bonds : bond 0.05347 ( 861) hydrogen bonds : angle 4.42051 ( 2472) *********************** 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 230 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 140 time to evaluate : 0.883 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: A 14 GLN cc_start: 0.4484 (OUTLIER) cc_final: 0.4190 (pp30) REVERT: A 50 SER cc_start: 0.9255 (m) cc_final: 0.9004 (t) REVERT: A 270 LEU cc_start: 0.9363 (mp) cc_final: 0.9053 (mp) REVERT: A 786 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8127 (tppt) REVERT: A 964 LYS cc_start: 0.9526 (OUTLIER) cc_final: 0.9143 (ttpp) REVERT: B 135 PHE cc_start: 0.7469 (m-80) cc_final: 0.7035 (m-80) REVERT: B 141 LEU cc_start: 0.9325 (mt) cc_final: 0.8413 (tt) REVERT: B 200 TYR cc_start: 0.9299 (m-80) cc_final: 0.8725 (m-80) REVERT: B 223 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7867 (mm) REVERT: B 228 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8553 (t0) REVERT: B 1028 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8741 (ttmt) REVERT: C 141 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8690 (tt) REVERT: C 238 PHE cc_start: 0.8395 (p90) cc_final: 0.7528 (p90) REVERT: C 242 LEU cc_start: 0.8700 (mm) cc_final: 0.8060 (tp) REVERT: C 456 PHE cc_start: 0.7998 (t80) cc_final: 0.7512 (t80) REVERT: C 460 ASN cc_start: 0.9165 (m-40) cc_final: 0.8285 (t0) REVERT: C 773 GLU cc_start: 0.8629 (tp30) cc_final: 0.8282 (tm-30) REVERT: C 984 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7504 (tp) REVERT: C 1107 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8057 (mtt180) outliers start: 90 outliers final: 51 residues processed: 221 average time/residue: 0.1362 time to fit residues: 50.5967 Evaluate side-chains 178 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 119 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 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 483 VAL 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 896 ILE Chi-restraints excluded: chain A residue 938 LEU 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 119 ILE 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 312 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 505 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 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 54 LEU 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 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 865 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1030 SER 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 256 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 253 optimal weight: 0.6980 chunk 285 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 274 optimal weight: 0.2980 chunk 156 optimal weight: 20.0000 chunk 194 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 188 ASN A 207 HIS B 69 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.086010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.058873 restraints weight = 110427.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.060733 restraints weight = 52912.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.061307 restraints weight = 29846.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.061494 restraints weight = 30342.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.061570 restraints weight = 25222.002| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 25720 Z= 0.103 Angle : 0.492 12.538 35025 Z= 0.247 Chirality : 0.041 0.144 3953 Planarity : 0.003 0.048 4539 Dihedral : 3.493 46.868 3445 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 2.14 % Allowed : 10.80 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.15), residues: 3171 helix: 2.06 (0.22), residues: 638 sheet: 0.22 (0.20), residues: 691 loop : -2.08 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 190 TYR 0.014 0.001 TYR C 756 PHE 0.011 0.001 PHE B1121 TRP 0.020 0.001 TRP C 436 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00228 (25678) covalent geometry : angle 0.49109 (34941) SS BOND : bond 0.00209 ( 42) SS BOND : angle 0.66335 ( 84) hydrogen bonds : bond 0.04398 ( 861) hydrogen bonds : angle 4.04490 ( 2472) *********************** 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 194 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 134 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.4222 (OUTLIER) cc_final: 0.3668 (pp30) REVERT: A 270 LEU cc_start: 0.9370 (mp) cc_final: 0.9088 (mp) REVERT: A 786 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8114 (tppt) REVERT: A 964 LYS cc_start: 0.9470 (OUTLIER) cc_final: 0.9165 (ttmm) REVERT: B 141 LEU cc_start: 0.9269 (mt) cc_final: 0.8303 (tt) REVERT: B 200 TYR cc_start: 0.9322 (m-80) cc_final: 0.8762 (m-80) REVERT: B 223 LEU cc_start: 0.8166 (mm) cc_final: 0.7872 (mm) REVERT: C 141 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8765 (tp) REVERT: C 238 PHE cc_start: 0.8417 (p90) cc_final: 0.7592 (p90) REVERT: C 242 LEU cc_start: 0.8758 (mm) cc_final: 0.8417 (tp) REVERT: C 456 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7368 (t80) REVERT: C 460 ASN cc_start: 0.9164 (m-40) cc_final: 0.8241 (t0) REVERT: C 855 PHE cc_start: 0.8079 (m-10) cc_final: 0.7727 (m-80) REVERT: C 984 LEU cc_start: 0.8234 (mm) cc_final: 0.7565 (tp) REVERT: C 1107 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7993 (mtt180) outliers start: 60 outliers final: 38 residues processed: 186 average time/residue: 0.1339 time to fit residues: 41.1501 Evaluate side-chains 159 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 312 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR 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 740 MET 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 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 193 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 505 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 938 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 390 LEU Chi-restraints excluded: chain C residue 456 PHE 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 1107 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 26 optimal weight: 4.9990 chunk 253 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 270 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 564 GLN B 66 HIS B 69 HIS B 360 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.082097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.053106 restraints weight = 112545.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.055843 restraints weight = 56343.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.056450 restraints weight = 28473.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.056900 restraints weight = 22138.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.056853 restraints weight = 22359.107| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 25720 Z= 0.227 Angle : 0.611 10.915 35025 Z= 0.311 Chirality : 0.043 0.145 3953 Planarity : 0.004 0.088 4539 Dihedral : 4.036 46.950 3445 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.40 % Favored : 93.57 % Rotamer: Outliers : 2.92 % Allowed : 10.84 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.15), residues: 3171 helix: 1.68 (0.21), residues: 633 sheet: 0.15 (0.19), residues: 702 loop : -2.03 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 44 TYR 0.031 0.002 TYR C 904 PHE 0.026 0.002 PHE C 782 TRP 0.015 0.001 TRP A1102 HIS 0.008 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00524 (25678) covalent geometry : angle 0.61032 (34941) SS BOND : bond 0.00235 ( 42) SS BOND : angle 0.83487 ( 84) hydrogen bonds : bond 0.05763 ( 861) hydrogen bonds : angle 4.53992 ( 2472) *********************** 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 189 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 107 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8698 (mt) cc_final: 0.7626 (tp) REVERT: A 270 LEU cc_start: 0.9394 (mp) cc_final: 0.9153 (mp) REVERT: A 964 LYS cc_start: 0.9488 (OUTLIER) cc_final: 0.9132 (ttpp) REVERT: B 141 LEU cc_start: 0.9400 (mt) cc_final: 0.8493 (tt) REVERT: B 200 TYR cc_start: 0.9404 (m-80) cc_final: 0.8789 (m-80) REVERT: B 223 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8073 (mm) REVERT: B 1028 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8771 (ttmt) REVERT: C 141 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8770 (tp) REVERT: C 177 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.8025 (pmm) REVERT: C 238 PHE cc_start: 0.8412 (p90) cc_final: 0.7559 (p90) REVERT: C 242 LEU cc_start: 0.8980 (mm) cc_final: 0.8255 (tp) REVERT: C 456 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7636 (t80) REVERT: C 460 ASN cc_start: 0.9276 (m-40) cc_final: 0.8960 (m-40) REVERT: C 773 GLU cc_start: 0.8715 (tp30) cc_final: 0.8169 (tm-30) REVERT: C 855 PHE cc_start: 0.8104 (m-10) cc_final: 0.7767 (m-80) REVERT: C 984 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7766 (tp) REVERT: C 1107 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7971 (mtt180) outliers start: 82 outliers final: 59 residues processed: 178 average time/residue: 0.1319 time to fit residues: 39.6964 Evaluate side-chains 167 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 100 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 118 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 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 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 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 938 LEU 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 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 380 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 560 LEU 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 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 51 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 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 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 984 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 273 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 290 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 216 optimal weight: 6.9990 chunk 144 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 580 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C 536 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.080219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.051333 restraints weight = 112290.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.053987 restraints weight = 56013.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.054609 restraints weight = 28440.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.055057 restraints weight = 22337.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.055013 restraints weight = 22725.076| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.6332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 25720 Z= 0.259 Angle : 0.648 12.920 35025 Z= 0.333 Chirality : 0.044 0.208 3953 Planarity : 0.004 0.083 4539 Dihedral : 4.437 47.631 3445 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 3.21 % Allowed : 10.91 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.15), residues: 3171 helix: 1.45 (0.21), residues: 640 sheet: 0.05 (0.19), residues: 738 loop : -2.12 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1107 TYR 0.039 0.002 TYR B 904 PHE 0.023 0.002 PHE A 759 TRP 0.014 0.002 TRP A1102 HIS 0.008 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00593 (25678) covalent geometry : angle 0.64685 (34941) SS BOND : bond 0.00313 ( 42) SS BOND : angle 0.90619 ( 84) hydrogen bonds : bond 0.06100 ( 861) hydrogen bonds : angle 4.80311 ( 2472) *********************** 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 194 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 104 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8920 (mt) cc_final: 0.7990 (tp) REVERT: A 964 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9090 (ttpp) REVERT: B 141 LEU cc_start: 0.9328 (mt) cc_final: 0.8398 (tt) REVERT: B 200 TYR cc_start: 0.9492 (m-80) cc_final: 0.8722 (m-80) REVERT: C 141 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8822 (tp) REVERT: C 177 MET cc_start: 0.8638 (mpp) cc_final: 0.8358 (mpp) REVERT: C 238 PHE cc_start: 0.8460 (p90) cc_final: 0.7584 (p90) REVERT: C 242 LEU cc_start: 0.8982 (mm) cc_final: 0.8250 (tp) REVERT: C 338 PHE cc_start: 0.8969 (m-10) cc_final: 0.8723 (m-10) REVERT: C 456 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.7775 (t80) REVERT: C 773 GLU cc_start: 0.8737 (tp30) cc_final: 0.8082 (tm-30) REVERT: C 855 PHE cc_start: 0.8157 (m-10) cc_final: 0.7766 (m-80) REVERT: C 906 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.7495 (t80) REVERT: C 984 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.7781 (tp) REVERT: C 1107 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8056 (mtt180) outliers start: 90 outliers final: 65 residues processed: 184 average time/residue: 0.1291 time to fit residues: 40.5241 Evaluate side-chains 163 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 92 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 934 ILE Chi-restraints excluded: chain A residue 938 LEU 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 119 ILE 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 480 CYS Chi-restraints excluded: chain B residue 560 LEU 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 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 345 THR 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 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 984 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.9254 > 50: distance: 66 - 73: 34.912 distance: 67 - 94: 35.158 distance: 73 - 74: 56.983 distance: 74 - 75: 38.588 distance: 75 - 76: 40.827 distance: 75 - 81: 40.142 distance: 76 - 106: 56.855 distance: 78 - 80: 39.912 distance: 81 - 82: 42.706 distance: 82 - 83: 43.755 distance: 82 - 85: 44.740 distance: 83 - 86: 39.728 distance: 86 - 87: 40.142 distance: 87 - 88: 56.587 distance: 87 - 90: 39.041 distance: 91 - 92: 56.451 distance: 94 - 95: 40.088 distance: 95 - 96: 39.107 distance: 95 - 98: 41.427 distance: 96 - 97: 39.484 distance: 96 - 106: 57.828 distance: 99 - 100: 56.812 distance: 99 - 101: 38.753 distance: 100 - 102: 40.453 distance: 101 - 103: 40.761 distance: 102 - 104: 38.508 distance: 103 - 104: 56.895 distance: 104 - 105: 56.391 distance: 106 - 107: 39.042 distance: 107 - 108: 39.558 distance: 107 - 110: 70.528 distance: 108 - 114: 45.453 distance: 110 - 111: 56.634 distance: 111 - 113: 60.214 distance: 114 - 115: 43.476 distance: 116 - 126: 56.458 distance: 118 - 119: 5.776 distance: 119 - 120: 66.870 distance: 119 - 121: 33.009 distance: 120 - 122: 40.178 distance: 121 - 123: 39.835 distance: 122 - 124: 31.317 distance: 123 - 124: 41.383 distance: 124 - 125: 56.975 distance: 126 - 127: 39.443 distance: 127 - 128: 61.192 distance: 127 - 130: 39.944 distance: 128 - 129: 44.518 distance: 128 - 135: 44.668 distance: 130 - 131: 41.211 distance: 131 - 132: 38.951 distance: 132 - 133: 39.844 distance: 133 - 134: 40.171 distance: 135 - 136: 56.047 distance: 136 - 139: 40.829 distance: 137 - 138: 40.319 distance: 137 - 143: 38.999 distance: 140 - 141: 56.648 distance: 143 - 144: 56.321 distance: 143 - 149: 57.533 distance: 144 - 145: 38.547 distance: 145 - 146: 40.152 distance: 145 - 150: 57.118 distance: 147 - 148: 39.608 distance: 148 - 149: 39.784 distance: 150 - 151: 15.103 distance: 151 - 152: 43.633 distance: 151 - 154: 16.985 distance: 152 - 153: 39.022 distance: 152 - 158: 35.918 distance: 154 - 155: 38.579 distance: 155 - 157: 56.973