Starting phenix.real_space_refine on Sat Feb 7 13:05:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s0d_24787/02_2026/7s0d_24787.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s0d_24787/02_2026/7s0d_24787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s0d_24787/02_2026/7s0d_24787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s0d_24787/02_2026/7s0d_24787.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s0d_24787/02_2026/7s0d_24787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s0d_24787/02_2026/7s0d_24787.map" } resolution = 3.5 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= -0.000 sd= 0.023 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 149 5.16 5 C 21388 2.51 5 N 5604 2.21 5 O 6482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33623 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7844 Classifications: {'peptide': 1013} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 54, 'TRANS': 958} Chain breaks: 9 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 5, 'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 7976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7976 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 55, 'TRANS': 977} Chain breaks: 10 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 7882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7882 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 54, 'TRANS': 971} Chain breaks: 10 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 5, 'TYR:plan': 3, 'ASP:plan': 8, 'PHE:plan': 2, 'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "H" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1657 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "L" Number of atoms: 1650 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1678 Chain: "M" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1657 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "N" Number of atoms: 1650 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1678 Chain: "O" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1657 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "P" Number of atoms: 1650 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1678 Time building chain proxies: 7.79, per 1000 atoms: 0.23 Number of scatterers: 33623 At special positions: 0 Unit cell: (239.844, 231.154, 181.621, 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 149 16.00 O 6482 8.00 N 5604 7.00 C 21388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, 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 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.04 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 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=2.02 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 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 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG ACYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG BCYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 148 " - pdb=" SG CYS M 204 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG ACYS N 194 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG BCYS N 194 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 148 " - pdb=" SG CYS O 204 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG ACYS P 194 " distance=2.04 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG BCYS P 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8200 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 73 sheets defined 19.6% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.634A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.488A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.731A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.926A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.775A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.317A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.734A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.301A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 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 removed outlier: 3.920A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.903A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.545A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.513A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 811 through 815 removed outlier: 4.174A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.568A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.542A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.548A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.607A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.563A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.773A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.293A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.668A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.445A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.081A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.384A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.197A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) 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 removed outlier: 3.697A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.472A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.287A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.658A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'L' and resid 121 through 127 removed outlier: 4.085A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 188 Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.685A pdb=" N THR M 91 " --> pdb=" O ALA M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 197 No H-bonds generated for 'chain 'M' and resid 195 through 197' Processing helix chain 'N' and resid 121 through 128 removed outlier: 4.216A pdb=" N SER N 127 " --> pdb=" O GLU N 123 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY N 128 " --> pdb=" O GLN N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 182 through 188 Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.713A pdb=" N THR O 91 " --> pdb=" O ALA O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 197 No H-bonds generated for 'chain 'O' and resid 195 through 197' Processing helix chain 'P' and resid 121 through 127 removed outlier: 4.072A pdb=" N SER P 127 " --> pdb=" O GLU P 123 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.437A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.514A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.249A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 10.597A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.744A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.625A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.534A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.573A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.358A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.498A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.723A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.102A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.563A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.585A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 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 1120 through 1121 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 29 through 30 removed outlier: 8.496A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 226 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.063A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 10.726A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.669A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.692A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 8.723A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.280A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.776A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.897A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.680A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 718 removed outlier: 6.786A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 721 through 727 removed outlier: 6.350A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 721 through 727 Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 29 through 30 removed outlier: 8.398A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.978A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 10.661A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.519A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.027A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.627A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.428A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.965A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.801A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.959A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.959A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.237A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AF2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.623A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.357A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 128 through 132 removed outlier: 4.234A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA H 145 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL H 192 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLY H 147 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL H 190 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N SER H 188 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 128 through 132 removed outlier: 4.234A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA H 145 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL H 192 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLY H 147 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL H 190 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N SER H 188 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER H 185 " --> pdb=" O VAL H 177 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL H 177 " --> pdb=" O SER H 185 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 158 through 159 removed outlier: 3.529A pdb=" N THR H 159 " --> pdb=" O ASN H 207 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.991A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.630A pdb=" N PHE L 116 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR L 172 " --> pdb=" O GLN L 166 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLN L 166 " --> pdb=" O THR L 172 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER L 174 " --> pdb=" O THR L 164 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.910A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR L 197 " --> pdb=" O LYS L 145 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.790A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER M 25 " --> pdb=" O GLN M 3 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU M 18 " --> pdb=" O MET M 83 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.733A pdb=" N VAL M 12 " --> pdb=" O THR M 118 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 128 through 132 removed outlier: 3.840A pdb=" N GLY M 147 " --> pdb=" O LEU M 132 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TYR M 184 " --> pdb=" O ASP M 152 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 128 through 132 removed outlier: 3.840A pdb=" N GLY M 147 " --> pdb=" O LEU M 132 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TYR M 184 " --> pdb=" O ASP M 152 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 158 through 162 Processing sheet with id=AG7, first strand: chain 'N' and resid 6 through 7 Processing sheet with id=AG8, first strand: chain 'N' and resid 10 through 14 removed outlier: 6.196A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS N 107 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA N 13 " --> pdb=" O LYS N 107 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 19 through 20 removed outlier: 3.581A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 114 through 118 removed outlier: 3.798A pdb=" N PHE N 116 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA N 130 " --> pdb=" O LEU N 181 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR N 173 " --> pdb=" O ASN N 138 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N THR N 172 " --> pdb=" O GLN N 166 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLN N 166 " --> pdb=" O THR N 172 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER N 174 " --> pdb=" O THR N 164 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 153 through 154 removed outlier: 3.888A pdb=" N LYS N 145 " --> pdb=" O THR N 197 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.762A pdb=" N LEU O 18 " --> pdb=" O MET O 83 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.723A pdb=" N VAL O 12 " --> pdb=" O THR O 118 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N MET O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N TYR O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 128 through 131 removed outlier: 5.067A pdb=" N ALA O 145 " --> pdb=" O VAL O 192 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL O 192 " --> pdb=" O ALA O 145 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLY O 147 " --> pdb=" O VAL O 190 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL O 190 " --> pdb=" O GLY O 147 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU O 149 " --> pdb=" O SER O 188 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N SER O 188 " --> pdb=" O LEU O 149 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LYS O 151 " --> pdb=" O LEU O 186 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU O 186 " --> pdb=" O LYS O 151 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR O 153 " --> pdb=" O TYR O 184 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 158 through 162 Processing sheet with id=AH7, first strand: chain 'P' and resid 5 through 7 Processing sheet with id=AH8, first strand: chain 'P' and resid 10 through 14 removed outlier: 4.149A pdb=" N LEU P 11 " --> pdb=" O LYS P 103 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU P 105 " --> pdb=" O LEU P 11 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'P' and resid 114 through 118 removed outlier: 3.633A pdb=" N PHE P 116 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL P 132 " --> pdb=" O LEU P 179 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS P 134 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER P 177 " --> pdb=" O CYS P 134 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU P 136 " --> pdb=" O LEU P 175 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU P 175 " --> pdb=" O LEU P 136 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR P 172 " --> pdb=" O GLN P 166 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLN P 166 " --> pdb=" O THR P 172 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER P 174 " --> pdb=" O THR P 164 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'P' and resid 153 through 154 removed outlier: 3.589A pdb=" N TYR P 192 " --> pdb=" O PHE P 209 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS P 207 " --> pdb=" O CYS P 194 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL P 196 " --> pdb=" O VAL P 205 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL P 205 " --> pdb=" O VAL P 196 " (cutoff:3.500A) 1333 hydrogen bonds defined for protein. 3546 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: 8.82 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10831 1.35 - 1.48: 8984 1.48 - 1.61: 14389 1.61 - 1.75: 7 1.75 - 1.88: 183 Bond restraints: 34394 Sorted by residual: bond pdb=" N PRO P 40 " pdb=" CD PRO P 40 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.22e+01 bond pdb=" CB PRO P 40 " pdb=" CG PRO P 40 " ideal model delta sigma weight residual 1.492 1.657 -0.165 5.00e-02 4.00e+02 1.09e+01 bond pdb=" CB PRO B1079 " pdb=" CG PRO B1079 " ideal model delta sigma weight residual 1.492 1.629 -0.137 5.00e-02 4.00e+02 7.48e+00 bond pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " ideal model delta sigma weight residual 1.808 1.726 0.082 3.30e-02 9.18e+02 6.12e+00 bond pdb=" C LEU P 78 " pdb=" N GLN P 79 " ideal model delta sigma weight residual 1.339 1.472 -0.132 5.57e-02 3.22e+02 5.64e+00 ... (remaining 34389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.97: 46688 4.97 - 9.95: 152 9.95 - 14.92: 13 14.92 - 19.89: 0 19.89 - 24.86: 1 Bond angle restraints: 46854 Sorted by residual: angle pdb=" CA CYS C 649 " pdb=" CB CYS C 649 " pdb=" SG CYS C 649 " ideal model delta sigma weight residual 114.40 139.26 -24.86 2.30e+00 1.89e-01 1.17e+02 angle pdb=" CA PRO P 40 " pdb=" N PRO P 40 " pdb=" CD PRO P 40 " ideal model delta sigma weight residual 112.00 100.28 11.72 1.40e+00 5.10e-01 7.01e+01 angle pdb=" CA PRO B1079 " pdb=" N PRO B1079 " pdb=" CD PRO B1079 " ideal model delta sigma weight residual 112.00 100.48 11.52 1.40e+00 5.10e-01 6.77e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 128.04 -13.64 2.30e+00 1.89e-01 3.52e+01 angle pdb=" CA PRO N 80 " pdb=" N PRO N 80 " pdb=" CD PRO N 80 " ideal model delta sigma weight residual 112.00 104.08 7.92 1.40e+00 5.10e-01 3.20e+01 ... (remaining 46849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 18772 17.93 - 35.87: 1375 35.87 - 53.80: 284 53.80 - 71.73: 56 71.73 - 89.67: 34 Dihedral angle restraints: 20521 sinusoidal: 7782 harmonic: 12739 Sorted by residual: dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -170.90 84.90 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -14.70 -71.30 1 1.00e+01 1.00e-02 6.52e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 159.52 -66.52 1 1.00e+01 1.00e-02 5.77e+01 ... (remaining 20518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 5065 0.106 - 0.212: 280 0.212 - 0.317: 11 0.317 - 0.423: 2 0.423 - 0.529: 1 Chirality restraints: 5359 Sorted by residual: chirality pdb=" CA CYS C 649 " pdb=" N CYS C 649 " pdb=" C CYS C 649 " pdb=" CB CYS C 649 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" CB ILE C 105 " pdb=" CA ILE C 105 " pdb=" CG1 ILE C 105 " pdb=" CG2 ILE C 105 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 5356 not shown) Planarity restraints: 6046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN N 79 " 0.111 5.00e-02 4.00e+02 1.63e-01 4.28e+01 pdb=" N PRO N 80 " -0.283 5.00e-02 4.00e+02 pdb=" CA PRO N 80 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO N 80 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 101 " 0.044 2.00e-02 2.50e+03 3.70e-02 3.43e+01 pdb=" CG TRP H 101 " -0.099 2.00e-02 2.50e+03 pdb=" CD1 TRP H 101 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP H 101 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 101 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 101 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 101 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 101 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 101 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP H 101 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS P 39 " -0.102 5.00e-02 4.00e+02 1.44e-01 3.34e+01 pdb=" N PRO P 40 " 0.249 5.00e-02 4.00e+02 pdb=" CA PRO P 40 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO P 40 " -0.074 5.00e-02 4.00e+02 ... (remaining 6043 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 285 2.56 - 3.14: 27733 3.14 - 3.73: 51229 3.73 - 4.31: 70402 4.31 - 4.90: 117112 Nonbonded interactions: 266761 Sorted by model distance: nonbonded pdb=" O ARG A 214 " pdb=" OH TYR A 266 " model vdw 1.969 3.040 nonbonded pdb=" O GLN A 755 " pdb=" OG SER C 968 " model vdw 2.020 3.040 nonbonded pdb=" O LEU B 966 " pdb=" OG SER B 975 " model vdw 2.044 3.040 nonbonded pdb=" OH TYR A 200 " pdb=" ND2 ASN C 394 " model vdw 2.063 3.120 nonbonded pdb=" O ILE A 101 " pdb=" NH2 ARG A 190 " model vdw 2.072 3.120 ... (remaining 266756 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 331 or (resid 332 through 335 and (name N or na \ me CA or name C or name O or name CB )) or resid 336 through 344 or (resid 345 t \ hrough 346 and (name N or name CA or name C or name O or name CB )) or resid 347 \ through 350 or (resid 351 through 352 and (name N or name CA or name C or name \ O or name CB )) or resid 353 through 363 or (resid 364 and (name N or name CA or \ name C or name O or name CB )) or resid 365 through 368 or (resid 369 and (name \ N or name CA or name C or name O or name CB )) or resid 370 through 373 or (res \ id 374 and (name N or name CA or name C or name O or name CB )) or resid 375 thr \ ough 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) \ or resid 409 through 441 or (resid 442 and (name N or name CA or name C or name \ O or name CB )) or resid 443 or (resid 449 and (name N or name CA or name C or n \ ame O or name CB )) or resid 450 through 496 or (resid 497 through 498 and (name \ N or name CA or name C or name O or name CB )) or resid 503 through 504 or (res \ id 505 and (name N or name CA or name C or name O or name CB )) or resid 506 thr \ ough 508 or (resid 509 and (name N or name CA or name C or name O or name CB )) \ or resid 510 through 620 or resid 641 through 1146)) selection = (chain 'B' and (resid 14 through 333 or (resid 334 through 335 and (name N or na \ me CA or name C or name O or name CB )) or resid 336 through 348 or (resid 349 a \ nd (name N or name CA or name C or name O or name CB )) or resid 350 or (resid 3 \ 51 through 352 and (name N or name CA or name C or name O or name CB )) or resid \ 353 through 363 or (resid 364 and (name N or name CA or name C or name O or nam \ e CB )) or resid 365 through 373 or (resid 374 and (name N or name CA or name C \ or name O or name CB )) or resid 375 through 397 or (resid 398 and (name N or na \ me CA or name C or name O or name CB )) or resid 399 through 426 or (resid 427 t \ hrough 428 and (name N or name CA or name C or name O or name CB )) or resid 429 \ through 441 or (resid 442 and (name N or name CA or name C or name O or name CB \ )) or resid 443 through 454 or resid 491 or (resid 492 through 493 and (name N \ or name CA or name C or name O or name CB )) or resid 494 through 496 or (resid \ 497 through 498 and (name N or name CA or name C or name O or name CB )) or resi \ d 503 through 508 or (resid 509 and (name N or name CA or name C or name O or na \ me CB )) or resid 510 through 527 or (resid 528 through 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 through 620 or resid 641 throu \ gh 1146)) selection = (chain 'C' and (resid 14 through 344 or (resid 345 through 346 and (name N or na \ me CA or name C or name O or name CB )) or resid 347 through 454 or resid 491 th \ rough 504 or (resid 505 and (name N or name CA or name C or name O or name CB )) \ or resid 506 through 1146)) } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = (chain 'L' and (resid 1 through 193 or resid 195 through 214)) selection = (chain 'N' and (resid 1 through 193 or resid 195 through 214)) selection = (chain 'P' and (resid 1 through 193 or resid 195 through 214)) } 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=0.04 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 31.670 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 : 0.005 0.165 34448 Z= 0.189 Angle : 0.893 24.864 46962 Z= 0.480 Chirality : 0.053 0.529 5359 Planarity : 0.007 0.163 6046 Dihedral : 13.461 89.667 12159 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.01 % Favored : 93.36 % Rotamer: Outliers : 0.13 % Allowed : 0.62 % Favored : 99.25 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 4310 helix: 1.05 (0.20), residues: 712 sheet: -0.10 (0.15), residues: 1110 loop : -1.16 (0.12), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG O 38 TYR 0.062 0.002 TYR P 186 PHE 0.033 0.002 PHE A 157 TRP 0.099 0.004 TRP H 101 HIS 0.013 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00467 (34394) covalent geometry : angle 0.88200 (46854) SS BOND : bond 0.00542 ( 54) SS BOND : angle 3.09979 ( 108) hydrogen bonds : bond 0.15930 ( 1252) hydrogen bonds : angle 7.97163 ( 3546) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 459 time to evaluate : 1.272 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: A 202 LYS cc_start: 0.8414 (mttt) cc_final: 0.8146 (mttt) REVERT: A 224 GLU cc_start: 0.7645 (mp0) cc_final: 0.7413 (mp0) REVERT: A 586 ASP cc_start: 0.7179 (m-30) cc_final: 0.6928 (m-30) REVERT: B 65 PHE cc_start: 0.8428 (m-10) cc_final: 0.8169 (m-10) REVERT: B 354 ASN cc_start: 0.7674 (t0) cc_final: 0.7393 (t0) REVERT: B 755 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8399 (tm-30) REVERT: B 984 LEU cc_start: 0.8659 (tp) cc_final: 0.8284 (tp) REVERT: C 134 GLN cc_start: 0.7545 (tp40) cc_final: 0.6501 (mp10) REVERT: C 135 PHE cc_start: 0.6409 (m-10) cc_final: 0.6130 (m-10) REVERT: C 244 LEU cc_start: 0.7911 (mp) cc_final: 0.7699 (mp) REVERT: C 329 PHE cc_start: 0.7223 (m-10) cc_final: 0.6924 (m-80) REVERT: C 394 ASN cc_start: 0.8026 (p0) cc_final: 0.7747 (p0) REVERT: H 34 MET cc_start: 0.6511 (mmm) cc_final: 0.5820 (mmm) REVERT: H 50 TYR cc_start: 0.5320 (m-10) cc_final: 0.5008 (m-80) REVERT: H 70 ILE cc_start: 0.6421 (tt) cc_final: 0.6122 (tp) REVERT: H 106 LEU cc_start: 0.5340 (tt) cc_final: 0.4839 (tt) REVERT: L 4 MET cc_start: 0.6559 (mmp) cc_final: 0.6342 (mmp) REVERT: M 99 ASP cc_start: 0.6752 (p0) cc_final: 0.6110 (p0) REVERT: M 149 LEU cc_start: 0.5129 (tp) cc_final: 0.4773 (tp) REVERT: N 118 PHE cc_start: 0.3834 (m-80) cc_final: 0.3138 (m-80) REVERT: O 60 TYR cc_start: 0.7797 (m-80) cc_final: 0.7418 (m-80) REVERT: O 65 LYS cc_start: 0.7664 (mmmm) cc_final: 0.7440 (mmmm) REVERT: O 72 ARG cc_start: 0.4040 (ptp-110) cc_final: 0.3160 (ptm160) outliers start: 5 outliers final: 0 residues processed: 461 average time/residue: 0.1885 time to fit residues: 144.8615 Evaluate side-chains 282 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 755 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN A 613 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B1002 GLN C 804 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN M 82 GLN N 124 GLN O 179 GLN P 24 GLN P 166 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.146051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.104327 restraints weight = 94491.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.104302 restraints weight = 54650.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.104871 restraints weight = 33047.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.105153 restraints weight = 28671.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.105312 restraints weight = 25178.189| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 34448 Z= 0.207 Angle : 0.720 12.929 46962 Z= 0.379 Chirality : 0.048 0.223 5359 Planarity : 0.006 0.102 6046 Dihedral : 5.286 47.983 4670 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.73 % Favored : 94.03 % Rotamer: Outliers : 1.40 % Allowed : 7.82 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.13), residues: 4310 helix: 1.10 (0.20), residues: 703 sheet: -0.20 (0.15), residues: 1110 loop : -1.00 (0.12), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 19 TYR 0.045 0.002 TYR L 49 PHE 0.029 0.002 PHE A 133 TRP 0.043 0.003 TRP H 101 HIS 0.010 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00488 (34394) covalent geometry : angle 0.71378 (46854) SS BOND : bond 0.00715 ( 54) SS BOND : angle 2.05907 ( 108) hydrogen bonds : bond 0.04283 ( 1252) hydrogen bonds : angle 6.81260 ( 3546) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 323 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5935 (m-10) cc_final: 0.5681 (m-10) REVERT: A 177 MET cc_start: 0.4716 (mpp) cc_final: 0.4354 (mmm) REVERT: A 224 GLU cc_start: 0.7753 (mp0) cc_final: 0.7325 (pm20) REVERT: A 321 GLN cc_start: 0.8435 (mm110) cc_final: 0.8107 (mm-40) REVERT: A 558 LYS cc_start: 0.6242 (pttt) cc_final: 0.6004 (pttt) REVERT: A 740 MET cc_start: 0.7056 (mtp) cc_final: 0.6517 (mtt) REVERT: A 931 ILE cc_start: 0.8788 (mm) cc_final: 0.8552 (mt) REVERT: B 354 ASN cc_start: 0.7675 (t0) cc_final: 0.7397 (t0) REVERT: B 755 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8322 (tm-30) REVERT: B 1125 ASN cc_start: 0.7717 (p0) cc_final: 0.7466 (p0) REVERT: C 134 GLN cc_start: 0.7576 (tp40) cc_final: 0.6593 (mp10) REVERT: C 244 LEU cc_start: 0.8093 (mp) cc_final: 0.7856 (mp) REVERT: C 287 ASP cc_start: 0.7485 (t0) cc_final: 0.7107 (m-30) REVERT: C 317 ASN cc_start: 0.6787 (t0) cc_final: 0.6450 (t0) REVERT: C 329 PHE cc_start: 0.7680 (m-10) cc_final: 0.7335 (m-80) REVERT: C 377 PHE cc_start: 0.8447 (t80) cc_final: 0.8143 (t80) REVERT: C 997 ILE cc_start: 0.9498 (tp) cc_final: 0.9198 (tt) REVERT: H 38 ARG cc_start: 0.7323 (mtm180) cc_final: 0.6718 (mmt180) REVERT: H 101 TRP cc_start: 0.4810 (p-90) cc_final: 0.3781 (p-90) REVERT: H 106 LEU cc_start: 0.5026 (tt) cc_final: 0.4360 (tt) REVERT: L 105 GLU cc_start: 0.5413 (mt-10) cc_final: 0.5146 (mt-10) REVERT: L 126 LYS cc_start: 0.3234 (pttp) cc_final: 0.2981 (ptpp) REVERT: M 34 MET cc_start: 0.6336 (mmm) cc_final: 0.5627 (ttm) REVERT: M 99 ASP cc_start: 0.7778 (p0) cc_final: 0.7212 (p0) REVERT: N 4 MET cc_start: 0.3318 (mtp) cc_final: 0.2544 (pmm) REVERT: N 73 PHE cc_start: 0.5789 (t80) cc_final: 0.5580 (t80) REVERT: N 118 PHE cc_start: 0.3511 (m-80) cc_final: 0.3022 (m-80) REVERT: O 60 TYR cc_start: 0.7886 (m-80) cc_final: 0.7489 (m-80) REVERT: O 99 ASP cc_start: 0.5601 (t0) cc_final: 0.5221 (t70) REVERT: O 101 TRP cc_start: 0.3430 (OUTLIER) cc_final: 0.2944 (p-90) outliers start: 52 outliers final: 33 residues processed: 358 average time/residue: 0.1902 time to fit residues: 114.5305 Evaluate side-chains 304 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 269 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain O residue 101 TRP Chi-restraints excluded: chain P residue 29 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 15 optimal weight: 9.9990 chunk 194 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 270 optimal weight: 2.9990 chunk 411 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 360 optimal weight: 20.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C 913 GLN C1088 HIS ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS M 163 ASN ** P 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.145398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.105208 restraints weight = 93972.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.104851 restraints weight = 52027.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.104364 restraints weight = 34258.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.104649 restraints weight = 34323.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.105658 restraints weight = 27057.128| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34448 Z= 0.177 Angle : 0.657 13.053 46962 Z= 0.342 Chirality : 0.046 0.184 5359 Planarity : 0.005 0.084 6046 Dihedral : 5.137 57.071 4670 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.39 % Favored : 94.40 % Rotamer: Outliers : 1.96 % Allowed : 10.96 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 4310 helix: 1.09 (0.20), residues: 711 sheet: -0.30 (0.15), residues: 1139 loop : -0.91 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 328 TYR 0.030 0.002 TYR P 49 PHE 0.020 0.002 PHE C 562 TRP 0.030 0.002 TRP H 105 HIS 0.024 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00409 (34394) covalent geometry : angle 0.65261 (46854) SS BOND : bond 0.00475 ( 54) SS BOND : angle 1.76766 ( 108) hydrogen bonds : bond 0.03948 ( 1252) hydrogen bonds : angle 6.46376 ( 3546) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 324 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5926 (m-80) cc_final: 0.5423 (m-10) REVERT: A 173 GLN cc_start: 0.7355 (tm-30) cc_final: 0.6676 (tm-30) REVERT: A 177 MET cc_start: 0.4676 (mpp) cc_final: 0.4399 (mmm) REVERT: A 278 LYS cc_start: 0.7974 (pttm) cc_final: 0.7717 (pttp) REVERT: A 558 LYS cc_start: 0.6361 (pttt) cc_final: 0.6056 (pttt) REVERT: A 740 MET cc_start: 0.6826 (mtp) cc_final: 0.6428 (mtt) REVERT: B 68 ILE cc_start: 0.6492 (tp) cc_final: 0.5891 (tp) REVERT: B 237 ARG cc_start: 0.7385 (ttm110) cc_final: 0.6968 (ttm110) REVERT: B 338 PHE cc_start: 0.8111 (m-80) cc_final: 0.7809 (m-80) REVERT: B 354 ASN cc_start: 0.7679 (t0) cc_final: 0.7372 (t0) REVERT: B 423 TYR cc_start: 0.8194 (t80) cc_final: 0.7834 (t80) REVERT: B 755 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8334 (tt0) REVERT: B 1125 ASN cc_start: 0.7693 (p0) cc_final: 0.7451 (p0) REVERT: C 216 LEU cc_start: 0.7281 (mt) cc_final: 0.6242 (pp) REVERT: C 244 LEU cc_start: 0.8108 (mp) cc_final: 0.7842 (mp) REVERT: C 317 ASN cc_start: 0.6902 (t0) cc_final: 0.6672 (t0) REVERT: C 556 ASN cc_start: 0.6007 (t0) cc_final: 0.5680 (t0) REVERT: C 997 ILE cc_start: 0.9506 (tp) cc_final: 0.9187 (tt) REVERT: H 38 ARG cc_start: 0.7444 (mtm180) cc_final: 0.6817 (mmt180) REVERT: H 60 TYR cc_start: 0.8134 (m-80) cc_final: 0.7785 (m-80) REVERT: H 101 TRP cc_start: 0.4326 (p-90) cc_final: 0.3246 (p-90) REVERT: L 4 MET cc_start: 0.5750 (mmp) cc_final: 0.5460 (mmp) REVERT: L 103 LYS cc_start: 0.4776 (tptt) cc_final: 0.4383 (ptpp) REVERT: L 105 GLU cc_start: 0.5468 (mt-10) cc_final: 0.5141 (mt-10) REVERT: L 126 LYS cc_start: 0.3267 (pttp) cc_final: 0.3029 (ptpp) REVERT: M 34 MET cc_start: 0.6424 (mmm) cc_final: 0.5768 (ttm) REVERT: M 99 ASP cc_start: 0.7873 (p0) cc_final: 0.7474 (p0) REVERT: N 118 PHE cc_start: 0.3640 (m-80) cc_final: 0.3061 (m-80) REVERT: O 60 TYR cc_start: 0.7831 (m-80) cc_final: 0.7436 (m-80) outliers start: 73 outliers final: 45 residues processed: 377 average time/residue: 0.1922 time to fit residues: 122.5700 Evaluate side-chains 331 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 285 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain O residue 101 TRP Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain P residue 29 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 255 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 430 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 413 optimal weight: 4.9990 chunk 314 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 394 optimal weight: 0.0020 chunk 64 optimal weight: 0.9980 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 422 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 955 ASN H 3 GLN H 172 HIS P 155 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.145001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.101631 restraints weight = 93540.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.103652 restraints weight = 50671.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.104068 restraints weight = 27966.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.104259 restraints weight = 25471.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.104465 restraints weight = 23190.876| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 34448 Z= 0.173 Angle : 0.640 11.700 46962 Z= 0.333 Chirality : 0.046 0.178 5359 Planarity : 0.005 0.077 6046 Dihedral : 5.050 54.762 4670 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.46 % Favored : 94.33 % Rotamer: Outliers : 2.36 % Allowed : 13.00 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.13), residues: 4310 helix: 1.07 (0.20), residues: 718 sheet: -0.22 (0.15), residues: 1158 loop : -0.85 (0.13), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 211 TYR 0.022 0.002 TYR H 50 PHE 0.021 0.002 PHE H 68 TRP 0.028 0.002 TRP H 105 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00407 (34394) covalent geometry : angle 0.63488 (46854) SS BOND : bond 0.00497 ( 54) SS BOND : angle 1.80533 ( 108) hydrogen bonds : bond 0.03765 ( 1252) hydrogen bonds : angle 6.27804 ( 3546) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 299 time to evaluate : 1.372 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: A 133 PHE cc_start: 0.5973 (m-80) cc_final: 0.5376 (m-10) REVERT: A 177 MET cc_start: 0.4767 (mpp) cc_final: 0.4528 (mmm) REVERT: A 224 GLU cc_start: 0.7855 (mp0) cc_final: 0.7451 (pm20) REVERT: A 558 LYS cc_start: 0.6388 (pttt) cc_final: 0.5990 (pttt) REVERT: A 740 MET cc_start: 0.7029 (mtp) cc_final: 0.6756 (mtt) REVERT: B 66 HIS cc_start: 0.6805 (OUTLIER) cc_final: 0.6110 (p-80) REVERT: B 68 ILE cc_start: 0.5740 (tp) cc_final: 0.5109 (tp) REVERT: B 237 ARG cc_start: 0.7522 (ttm110) cc_final: 0.7057 (ttm110) REVERT: B 338 PHE cc_start: 0.8155 (m-80) cc_final: 0.7885 (m-80) REVERT: B 354 ASN cc_start: 0.7693 (t0) cc_final: 0.7344 (t0) REVERT: B 755 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8367 (tt0) REVERT: B 1125 ASN cc_start: 0.7705 (p0) cc_final: 0.7490 (p0) REVERT: C 216 LEU cc_start: 0.7406 (mt) cc_final: 0.6255 (pp) REVERT: C 244 LEU cc_start: 0.8063 (mp) cc_final: 0.7763 (mp) REVERT: C 997 ILE cc_start: 0.9533 (tp) cc_final: 0.9246 (tt) REVERT: H 34 MET cc_start: 0.7012 (mmm) cc_final: 0.6610 (mmm) REVERT: H 38 ARG cc_start: 0.7496 (mtm180) cc_final: 0.6808 (mmt180) REVERT: H 60 TYR cc_start: 0.8145 (m-80) cc_final: 0.7777 (m-80) REVERT: H 101 TRP cc_start: 0.4548 (p-90) cc_final: 0.3259 (p-90) REVERT: H 116 LEU cc_start: 0.7036 (tp) cc_final: 0.6637 (pt) REVERT: L 126 LYS cc_start: 0.3346 (pttp) cc_final: 0.3113 (ptpp) REVERT: M 99 ASP cc_start: 0.7813 (p0) cc_final: 0.7538 (p0) REVERT: N 4 MET cc_start: 0.3379 (mtp) cc_final: 0.3071 (ptp) REVERT: N 118 PHE cc_start: 0.3634 (m-80) cc_final: 0.2955 (m-80) REVERT: N 147 GLN cc_start: 0.6258 (mt0) cc_final: 0.5757 (mp10) REVERT: O 34 MET cc_start: 0.7179 (ttt) cc_final: 0.6819 (ttt) REVERT: O 60 TYR cc_start: 0.7914 (m-80) cc_final: 0.7576 (m-80) outliers start: 88 outliers final: 67 residues processed: 367 average time/residue: 0.1821 time to fit residues: 113.5493 Evaluate side-chains 337 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 268 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 101 TRP Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 354 optimal weight: 20.0000 chunk 145 optimal weight: 5.9990 chunk 383 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 361 optimal weight: 9.9990 chunk 399 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 321 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 422 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 360 ASN A 955 ASN A1108 ASN B 360 ASN B 914 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS H 205 ASN N 138 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.143348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.099736 restraints weight = 95557.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.101732 restraints weight = 48723.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.102637 restraints weight = 23520.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.102859 restraints weight = 20037.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.102950 restraints weight = 18346.138| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.118 34448 Z= 0.411 Angle : 0.850 14.001 46962 Z= 0.445 Chirality : 0.052 0.318 5359 Planarity : 0.006 0.083 6046 Dihedral : 5.848 50.690 4670 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.73 % Favored : 92.06 % Rotamer: Outliers : 4.00 % Allowed : 13.75 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.12), residues: 4310 helix: 0.60 (0.19), residues: 704 sheet: -0.49 (0.15), residues: 1147 loop : -1.24 (0.12), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 214 TYR 0.022 0.003 TYR A 904 PHE 0.032 0.003 PHE A 238 TRP 0.040 0.003 TRP H 105 HIS 0.011 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00950 (34394) covalent geometry : angle 0.84217 (46854) SS BOND : bond 0.00755 ( 54) SS BOND : angle 2.52932 ( 108) hydrogen bonds : bond 0.04766 ( 1252) hydrogen bonds : angle 6.88622 ( 3546) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 274 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6332 (m-80) cc_final: 0.5840 (m-10) REVERT: A 173 GLN cc_start: 0.7672 (tm-30) cc_final: 0.6940 (tm-30) REVERT: A 177 MET cc_start: 0.4479 (mpp) cc_final: 0.4239 (mmm) REVERT: A 224 GLU cc_start: 0.8246 (mp0) cc_final: 0.7891 (pm20) REVERT: A 365 TYR cc_start: 0.7687 (m-10) cc_final: 0.7274 (p90) REVERT: A 523 THR cc_start: 0.5452 (OUTLIER) cc_final: 0.5225 (t) REVERT: A 558 LYS cc_start: 0.6558 (pttt) cc_final: 0.5816 (pttt) REVERT: A 1089 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8565 (m-80) REVERT: B 66 HIS cc_start: 0.6807 (OUTLIER) cc_final: 0.6185 (p-80) REVERT: B 68 ILE cc_start: 0.5712 (tp) cc_final: 0.4981 (tp) REVERT: B 237 ARG cc_start: 0.7583 (ttm110) cc_final: 0.7193 (ttm110) REVERT: B 354 ASN cc_start: 0.7876 (t0) cc_final: 0.7479 (t0) REVERT: B 421 TYR cc_start: 0.5600 (OUTLIER) cc_final: 0.3880 (m-80) REVERT: C 421 TYR cc_start: 0.5264 (OUTLIER) cc_final: 0.3485 (m-80) REVERT: C 740 MET cc_start: 0.8099 (mtt) cc_final: 0.7687 (mtt) REVERT: C 997 ILE cc_start: 0.9591 (tp) cc_final: 0.9328 (tt) REVERT: H 34 MET cc_start: 0.7258 (mmm) cc_final: 0.6210 (mmp) REVERT: H 60 TYR cc_start: 0.8169 (m-80) cc_final: 0.7767 (m-80) REVERT: H 116 LEU cc_start: 0.7257 (tp) cc_final: 0.7011 (pt) REVERT: H 168 THR cc_start: 0.3495 (OUTLIER) cc_final: 0.3251 (t) REVERT: L 4 MET cc_start: 0.5919 (mmp) cc_final: 0.5604 (mmp) REVERT: L 105 GLU cc_start: 0.5587 (mt-10) cc_final: 0.5213 (mt-10) REVERT: M 99 ASP cc_start: 0.7966 (p0) cc_final: 0.7713 (p0) REVERT: O 60 TYR cc_start: 0.7899 (m-80) cc_final: 0.7544 (m-80) outliers start: 149 outliers final: 103 residues processed: 398 average time/residue: 0.1732 time to fit residues: 118.1293 Evaluate side-chains 354 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 245 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain M residue 50 TYR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 98 ARG Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 101 TRP Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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: 70.7087 > 50: distance: 20 - 26: 30.422 distance: 26 - 27: 11.648 distance: 27 - 28: 7.175 distance: 27 - 30: 36.453 distance: 28 - 29: 57.056 distance: 28 - 34: 38.906 distance: 30 - 31: 24.369 distance: 31 - 32: 36.228 distance: 31 - 33: 15.229 distance: 34 - 35: 16.893 distance: 35 - 36: 25.778 distance: 35 - 38: 15.781 distance: 36 - 37: 50.503 distance: 36 - 41: 9.702 distance: 38 - 39: 4.831 distance: 39 - 40: 7.057 distance: 41 - 42: 32.572 distance: 42 - 43: 33.001 distance: 42 - 45: 41.910 distance: 43 - 44: 40.219 distance: 45 - 46: 38.703 distance: 46 - 47: 31.659 distance: 46 - 48: 30.141 distance: 49 - 50: 46.200 distance: 49 - 55: 26.389 distance: 50 - 51: 23.415 distance: 50 - 53: 47.209 distance: 51 - 52: 35.182 distance: 51 - 56: 41.703 distance: 53 - 54: 6.166 distance: 54 - 55: 42.900 distance: 56 - 57: 35.910 distance: 57 - 58: 47.110 distance: 57 - 60: 25.377 distance: 58 - 59: 37.842 distance: 58 - 62: 40.825 distance: 60 - 61: 26.034 distance: 62 - 63: 18.050 distance: 63 - 64: 52.192 distance: 63 - 66: 40.754 distance: 64 - 65: 36.181 distance: 64 - 71: 35.888 distance: 66 - 67: 25.280 distance: 67 - 68: 7.984 distance: 68 - 69: 20.179 distance: 69 - 70: 9.572 distance: 71 - 72: 32.294 distance: 71 - 77: 25.203 distance: 72 - 73: 28.487 distance: 72 - 75: 13.277 distance: 73 - 74: 42.732 distance: 73 - 78: 19.039 distance: 75 - 76: 32.191 distance: 76 - 77: 18.700 distance: 78 - 79: 40.292 distance: 79 - 80: 42.150 distance: 79 - 82: 7.498 distance: 80 - 81: 38.850 distance: 80 - 84: 40.851 distance: 82 - 83: 28.826 distance: 84 - 85: 17.532 distance: 85 - 86: 33.163 distance: 85 - 88: 34.233 distance: 86 - 87: 27.829 distance: 86 - 93: 21.782 distance: 88 - 89: 13.474 distance: 89 - 90: 8.520 distance: 90 - 91: 28.303 distance: 91 - 92: 26.447 distance: 94 - 95: 18.874 distance: 94 - 97: 16.457 distance: 95 - 104: 35.133 distance: 97 - 98: 40.388 distance: 98 - 99: 18.358 distance: 99 - 100: 8.120 distance: 100 - 101: 7.014 distance: 101 - 102: 8.880 distance: 101 - 103: 8.568