Starting phenix.real_space_refine on Sat Mar 7 04:04:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pl9_13485/03_2026/7pl9_13485.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pl9_13485/03_2026/7pl9_13485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pl9_13485/03_2026/7pl9_13485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pl9_13485/03_2026/7pl9_13485.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pl9_13485/03_2026/7pl9_13485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pl9_13485/03_2026/7pl9_13485.map" } resolution = 3.21 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= 0.002 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 235 5.16 5 C 24990 2.51 5 N 6305 2.21 5 O 6415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37945 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7569 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 962} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 644 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'ASP:plan': 10, 'ASN:plan1': 5, 'GLN:plan1': 12, 'GLU:plan': 13, 'ARG:plan': 18, 'PHE:plan': 7, 'HIS:plan': 7, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 335 Chain: "B" Number of atoms: 7569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7569 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 962} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 644 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'ASP:plan': 10, 'ASN:plan1': 5, 'GLN:plan1': 12, 'GLU:plan': 13, 'ARG:plan': 18, 'PHE:plan': 7, 'HIS:plan': 7, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 335 Chain: "C" Number of atoms: 7569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7569 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 962} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 644 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'ASP:plan': 10, 'ASN:plan1': 5, 'GLN:plan1': 12, 'GLU:plan': 13, 'ARG:plan': 18, 'PHE:plan': 7, 'HIS:plan': 7, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 335 Chain: "D" Number of atoms: 7569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7569 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 962} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 644 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'ASP:plan': 10, 'ASN:plan1': 5, 'GLN:plan1': 12, 'GLU:plan': 13, 'ARG:plan': 18, 'PHE:plan': 7, 'HIS:plan': 7, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 335 Chain: "E" Number of atoms: 7569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7569 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 962} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 644 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'ASP:plan': 10, 'ASN:plan1': 5, 'GLN:plan1': 12, 'GLU:plan': 13, 'ARG:plan': 18, 'PHE:plan': 7, 'HIS:plan': 7, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 335 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 7.85, per 1000 atoms: 0.21 Number of scatterers: 37945 At special positions: 0 Unit cell: (184.9, 186.62, 121.26, 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 235 16.00 O 6415 8.00 N 6305 7.00 C 24990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.5 seconds 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9420 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 5 sheets defined 76.2% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 66 through 98 removed outlier: 3.565A pdb=" N ILE A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 112 through 141 removed outlier: 3.776A pdb=" N PHE A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 157 through 179 removed outlier: 4.197A pdb=" N VAL A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY A 177 " --> pdb=" O TYR A 173 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 217 removed outlier: 3.803A pdb=" N MET A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 244 removed outlier: 3.985A pdb=" N MET A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 275 removed outlier: 5.939A pdb=" N ALA A 251 " --> pdb=" O TRP A 247 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE A 252 " --> pdb=" O MET A 248 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A 253 " --> pdb=" O TRP A 249 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 312 removed outlier: 4.236A pdb=" N PHE A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 311 " --> pdb=" O MET A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 346 removed outlier: 3.978A pdb=" N TRP A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 384 removed outlier: 4.116A pdb=" N ALA A 352 " --> pdb=" O TRP A 348 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 491 removed outlier: 4.322A pdb=" N GLU A 473 " --> pdb=" O ILE A 469 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 495 Processing helix chain 'A' and resid 511 through 517 removed outlier: 3.806A pdb=" N PHE A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 541 Processing helix chain 'A' and resid 544 through 555 removed outlier: 3.541A pdb=" N ALA A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 578 removed outlier: 3.866A pdb=" N LEU A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 564 " --> pdb=" O GLY A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 616 removed outlier: 4.376A pdb=" N MET A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 603 " --> pdb=" O VAL A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 647 removed outlier: 3.697A pdb=" N VAL A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 636 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 647 " --> pdb=" O TRP A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 677 removed outlier: 4.534A pdb=" N PHE A 656 " --> pdb=" O TRP A 652 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 657 " --> pdb=" O TYR A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 715 removed outlier: 3.728A pdb=" N CYS A 693 " --> pdb=" O SER A 689 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 706 " --> pdb=" O TRP A 702 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 715 " --> pdb=" O VAL A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 748 removed outlier: 3.696A pdb=" N LYS A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 748 " --> pdb=" O MET A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 840 Processing helix chain 'A' and resid 846 through 853 removed outlier: 3.519A pdb=" N ARG A 850 " --> pdb=" O THR A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 866 removed outlier: 3.614A pdb=" N LEU A 859 " --> pdb=" O ARG A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 893 removed outlier: 4.030A pdb=" N THR A 883 " --> pdb=" O TRP A 879 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A 884 " --> pdb=" O GLU A 880 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 908 Processing helix chain 'A' and resid 918 through 937 removed outlier: 3.533A pdb=" N VAL A 922 " --> pdb=" O PHE A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 997 removed outlier: 3.672A pdb=" N HIS A 950 " --> pdb=" O SER A 946 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 952 " --> pdb=" O GLY A 948 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE A 953 " --> pdb=" O ILE A 949 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 965 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA A 968 " --> pdb=" O ARG A 964 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS A 970 " --> pdb=" O GLN A 966 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS A 971 " --> pdb=" O ALA A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1018 removed outlier: 3.792A pdb=" N ASN A1004 " --> pdb=" O GLU A1000 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1032 removed outlier: 4.203A pdb=" N LEU A1032 " --> pdb=" O ALA A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1044 Processing helix chain 'A' and resid 1048 through 1067 removed outlier: 3.679A pdb=" N TYR A1052 " --> pdb=" O ASN A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1094 removed outlier: 3.977A pdb=" N ILE A1077 " --> pdb=" O LEU A1073 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A1085 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A1086 " --> pdb=" O LYS A1082 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A1087 " --> pdb=" O ALA A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1122 removed outlier: 3.633A pdb=" N VAL A1103 " --> pdb=" O PRO A1099 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A1106 " --> pdb=" O TYR A1102 " (cutoff:3.500A) Proline residue: A1118 - end of helix Processing helix chain 'A' and resid 1126 through 1152 removed outlier: 3.588A pdb=" N LEU A1130 " --> pdb=" O GLY A1126 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN A1152 " --> pdb=" O VAL A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1186 removed outlier: 3.996A pdb=" N TYR A1166 " --> pdb=" O PRO A1162 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS A1167 " --> pdb=" O LEU A1163 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A1168 " --> pdb=" O ASP A1164 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A1179 " --> pdb=" O LEU A1175 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 98 removed outlier: 3.565A pdb=" N ILE B 88 " --> pdb=" O PHE B 84 " (cutoff:3.500A) Proline residue: B 95 - end of helix Processing helix chain 'B' and resid 112 through 141 removed outlier: 3.776A pdb=" N PHE B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 141 " --> pdb=" O LYS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 Processing helix chain 'B' and resid 157 through 179 removed outlier: 4.197A pdb=" N VAL B 161 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY B 177 " --> pdb=" O TYR B 173 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 217 removed outlier: 3.802A pdb=" N MET B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 244 removed outlier: 3.985A pdb=" N MET B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 275 removed outlier: 5.938A pdb=" N ALA B 251 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE B 253 " --> pdb=" O TRP B 249 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 312 removed outlier: 4.236A pdb=" N PHE B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 346 removed outlier: 3.978A pdb=" N TRP B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 384 removed outlier: 4.116A pdb=" N ALA B 352 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 361 " --> pdb=" O GLN B 357 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 491 removed outlier: 4.322A pdb=" N GLU B 473 " --> pdb=" O ILE B 469 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 495 Processing helix chain 'B' and resid 511 through 517 removed outlier: 3.806A pdb=" N PHE B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 541 Processing helix chain 'B' and resid 544 through 555 removed outlier: 3.542A pdb=" N ALA B 548 " --> pdb=" O ASP B 544 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 549 " --> pdb=" O PRO B 545 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN B 550 " --> pdb=" O ARG B 546 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 578 removed outlier: 3.866A pdb=" N LEU B 562 " --> pdb=" O ASN B 558 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 564 " --> pdb=" O GLY B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 616 removed outlier: 4.377A pdb=" N MET B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 603 " --> pdb=" O VAL B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 647 removed outlier: 3.696A pdb=" N VAL B 635 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B 636 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 647 " --> pdb=" O TRP B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 677 removed outlier: 4.535A pdb=" N PHE B 656 " --> pdb=" O TRP B 652 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 657 " --> pdb=" O TYR B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 715 removed outlier: 3.728A pdb=" N CYS B 693 " --> pdb=" O SER B 689 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 706 " --> pdb=" O TRP B 702 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 715 " --> pdb=" O VAL B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 748 removed outlier: 3.696A pdb=" N LYS B 736 " --> pdb=" O ASP B 732 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 748 " --> pdb=" O MET B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 840 Processing helix chain 'B' and resid 846 through 853 removed outlier: 3.519A pdb=" N ARG B 850 " --> pdb=" O THR B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 866 removed outlier: 3.614A pdb=" N LEU B 859 " --> pdb=" O ARG B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 893 removed outlier: 4.030A pdb=" N THR B 883 " --> pdb=" O TRP B 879 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG B 884 " --> pdb=" O GLU B 880 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 908 Processing helix chain 'B' and resid 918 through 937 removed outlier: 3.534A pdb=" N VAL B 922 " --> pdb=" O PHE B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 997 removed outlier: 3.673A pdb=" N HIS B 950 " --> pdb=" O SER B 946 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 952 " --> pdb=" O GLY B 948 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE B 953 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 965 " --> pdb=" O VAL B 961 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B 968 " --> pdb=" O ARG B 964 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS B 970 " --> pdb=" O GLN B 966 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS B 971 " --> pdb=" O ALA B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1018 removed outlier: 3.791A pdb=" N ASN B1004 " --> pdb=" O GLU B1000 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B1005 " --> pdb=" O ALA B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1032 removed outlier: 4.203A pdb=" N LEU B1032 " --> pdb=" O ALA B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1044 Processing helix chain 'B' and resid 1048 through 1067 removed outlier: 3.678A pdb=" N TYR B1052 " --> pdb=" O ASN B1048 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1094 removed outlier: 3.976A pdb=" N ILE B1077 " --> pdb=" O LEU B1073 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B1085 " --> pdb=" O ILE B1081 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B1086 " --> pdb=" O LYS B1082 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B1087 " --> pdb=" O ALA B1083 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1122 removed outlier: 3.633A pdb=" N VAL B1103 " --> pdb=" O PRO B1099 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B1106 " --> pdb=" O TYR B1102 " (cutoff:3.500A) Proline residue: B1118 - end of helix Processing helix chain 'B' and resid 1126 through 1152 removed outlier: 3.588A pdb=" N LEU B1130 " --> pdb=" O GLY B1126 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN B1152 " --> pdb=" O VAL B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1162 through 1186 removed outlier: 3.996A pdb=" N TYR B1166 " --> pdb=" O PRO B1162 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS B1167 " --> pdb=" O LEU B1163 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B1168 " --> pdb=" O ASP B1164 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP B1179 " --> pdb=" O LEU B1175 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 98 removed outlier: 3.565A pdb=" N ILE C 88 " --> pdb=" O PHE C 84 " (cutoff:3.500A) Proline residue: C 95 - end of helix Processing helix chain 'C' and resid 112 through 141 removed outlier: 3.777A pdb=" N PHE C 116 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C 141 " --> pdb=" O LYS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 155 Processing helix chain 'C' and resid 157 through 179 removed outlier: 4.197A pdb=" N VAL C 161 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY C 177 " --> pdb=" O TYR C 173 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 217 removed outlier: 3.802A pdb=" N MET C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 244 removed outlier: 3.984A pdb=" N MET C 226 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 275 removed outlier: 5.939A pdb=" N ALA C 251 " --> pdb=" O TRP C 247 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE C 252 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE C 253 " --> pdb=" O TRP C 249 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 312 removed outlier: 4.236A pdb=" N PHE C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN C 311 " --> pdb=" O MET C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 346 removed outlier: 3.978A pdb=" N TRP C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR C 346 " --> pdb=" O ALA C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 384 removed outlier: 4.116A pdb=" N ALA C 352 " --> pdb=" O TRP C 348 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA C 361 " --> pdb=" O GLN C 357 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 491 removed outlier: 4.322A pdb=" N GLU C 473 " --> pdb=" O ILE C 469 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 495 Processing helix chain 'C' and resid 511 through 517 removed outlier: 3.807A pdb=" N PHE C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 541 Processing helix chain 'C' and resid 544 through 555 removed outlier: 3.541A pdb=" N ALA C 548 " --> pdb=" O ASP C 544 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 549 " --> pdb=" O PRO C 545 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN C 550 " --> pdb=" O ARG C 546 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.866A pdb=" N LEU C 562 " --> pdb=" O ASN C 558 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 564 " --> pdb=" O GLY C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 616 removed outlier: 4.376A pdb=" N MET C 602 " --> pdb=" O ALA C 598 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 603 " --> pdb=" O VAL C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 647 removed outlier: 3.697A pdb=" N VAL C 635 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA C 636 " --> pdb=" O VAL C 632 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 647 " --> pdb=" O TRP C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 677 removed outlier: 4.534A pdb=" N PHE C 656 " --> pdb=" O TRP C 652 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 657 " --> pdb=" O TYR C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 715 removed outlier: 3.728A pdb=" N CYS C 693 " --> pdb=" O SER C 689 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 706 " --> pdb=" O TRP C 702 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 715 " --> pdb=" O VAL C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 748 removed outlier: 3.696A pdb=" N LYS C 736 " --> pdb=" O ASP C 732 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR C 748 " --> pdb=" O MET C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 840 Processing helix chain 'C' and resid 846 through 853 removed outlier: 3.520A pdb=" N ARG C 850 " --> pdb=" O THR C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 866 removed outlier: 3.613A pdb=" N LEU C 859 " --> pdb=" O ARG C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 893 removed outlier: 4.030A pdb=" N THR C 883 " --> pdb=" O TRP C 879 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG C 884 " --> pdb=" O GLU C 880 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 908 Processing helix chain 'C' and resid 918 through 937 removed outlier: 3.532A pdb=" N VAL C 922 " --> pdb=" O PHE C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 997 removed outlier: 3.673A pdb=" N HIS C 950 " --> pdb=" O SER C 946 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 952 " --> pdb=" O GLY C 948 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE C 953 " --> pdb=" O ILE C 949 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 965 " --> pdb=" O VAL C 961 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 968 " --> pdb=" O ARG C 964 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS C 970 " --> pdb=" O GLN C 966 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS C 971 " --> pdb=" O ALA C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1018 removed outlier: 3.792A pdb=" N ASN C1004 " --> pdb=" O GLU C1000 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C1005 " --> pdb=" O ALA C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1032 removed outlier: 4.203A pdb=" N LEU C1032 " --> pdb=" O ALA C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1044 Processing helix chain 'C' and resid 1048 through 1067 removed outlier: 3.679A pdb=" N TYR C1052 " --> pdb=" O ASN C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1094 removed outlier: 3.977A pdb=" N ILE C1077 " --> pdb=" O LEU C1073 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C1085 " --> pdb=" O ILE C1081 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN C1086 " --> pdb=" O LYS C1082 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C1087 " --> pdb=" O ALA C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1122 removed outlier: 3.633A pdb=" N VAL C1103 " --> pdb=" O PRO C1099 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C1106 " --> pdb=" O TYR C1102 " (cutoff:3.500A) Proline residue: C1118 - end of helix Processing helix chain 'C' and resid 1126 through 1152 removed outlier: 3.588A pdb=" N LEU C1130 " --> pdb=" O GLY C1126 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN C1152 " --> pdb=" O VAL C1148 " (cutoff:3.500A) Processing helix chain 'C' and resid 1162 through 1186 removed outlier: 3.996A pdb=" N TYR C1166 " --> pdb=" O PRO C1162 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS C1167 " --> pdb=" O LEU C1163 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C1168 " --> pdb=" O ASP C1164 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP C1179 " --> pdb=" O LEU C1175 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 98 removed outlier: 3.565A pdb=" N ILE D 88 " --> pdb=" O PHE D 84 " (cutoff:3.500A) Proline residue: D 95 - end of helix Processing helix chain 'D' and resid 112 through 141 removed outlier: 3.776A pdb=" N PHE D 116 " --> pdb=" O GLU D 112 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE D 135 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 Processing helix chain 'D' and resid 157 through 179 removed outlier: 4.196A pdb=" N VAL D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY D 177 " --> pdb=" O TYR D 173 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA D 178 " --> pdb=" O ILE D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 217 removed outlier: 3.802A pdb=" N MET D 199 " --> pdb=" O ALA D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 244 removed outlier: 3.984A pdb=" N MET D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 275 removed outlier: 5.939A pdb=" N ALA D 251 " --> pdb=" O TRP D 247 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE D 252 " --> pdb=" O MET D 248 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE D 253 " --> pdb=" O TRP D 249 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 312 removed outlier: 4.237A pdb=" N PHE D 310 " --> pdb=" O PHE D 306 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 346 removed outlier: 3.978A pdb=" N TRP D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR D 326 " --> pdb=" O GLN D 322 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR D 346 " --> pdb=" O ALA D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 384 removed outlier: 4.117A pdb=" N ALA D 352 " --> pdb=" O TRP D 348 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA D 361 " --> pdb=" O GLN D 357 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 491 removed outlier: 4.321A pdb=" N GLU D 473 " --> pdb=" O ILE D 469 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 495 Processing helix chain 'D' and resid 511 through 517 removed outlier: 3.805A pdb=" N PHE D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 541 Processing helix chain 'D' and resid 544 through 555 removed outlier: 3.540A pdb=" N ALA D 548 " --> pdb=" O ASP D 544 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 549 " --> pdb=" O PRO D 545 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN D 550 " --> pdb=" O ARG D 546 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 578 removed outlier: 3.866A pdb=" N LEU D 562 " --> pdb=" O ASN D 558 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 563 " --> pdb=" O LEU D 559 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA D 564 " --> pdb=" O GLY D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 616 removed outlier: 4.376A pdb=" N MET D 602 " --> pdb=" O ALA D 598 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU D 603 " --> pdb=" O VAL D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 647 removed outlier: 3.697A pdb=" N VAL D 635 " --> pdb=" O ILE D 631 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA D 636 " --> pdb=" O VAL D 632 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 647 " --> pdb=" O TRP D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 677 removed outlier: 4.534A pdb=" N PHE D 656 " --> pdb=" O TRP D 652 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 657 " --> pdb=" O TYR D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 715 removed outlier: 3.728A pdb=" N CYS D 693 " --> pdb=" O SER D 689 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY D 706 " --> pdb=" O TRP D 702 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA D 715 " --> pdb=" O VAL D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 748 removed outlier: 3.697A pdb=" N LYS D 736 " --> pdb=" O ASP D 732 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR D 748 " --> pdb=" O MET D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 829 through 840 Processing helix chain 'D' and resid 846 through 853 removed outlier: 3.520A pdb=" N ARG D 850 " --> pdb=" O THR D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 855 through 866 removed outlier: 3.614A pdb=" N LEU D 859 " --> pdb=" O ARG D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 879 through 893 removed outlier: 4.029A pdb=" N THR D 883 " --> pdb=" O TRP D 879 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG D 884 " --> pdb=" O GLU D 880 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS D 891 " --> pdb=" O THR D 887 " (cutoff:3.500A) Processing helix chain 'D' and resid 903 through 908 Processing helix chain 'D' and resid 918 through 937 removed outlier: 3.534A pdb=" N VAL D 922 " --> pdb=" O PHE D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 997 removed outlier: 3.673A pdb=" N HIS D 950 " --> pdb=" O SER D 946 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 952 " --> pdb=" O GLY D 948 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE D 953 " --> pdb=" O ILE D 949 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR D 965 " --> pdb=" O VAL D 961 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA D 968 " --> pdb=" O ARG D 964 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS D 970 " --> pdb=" O GLN D 966 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS D 971 " --> pdb=" O ALA D 967 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1018 removed outlier: 3.792A pdb=" N ASN D1004 " --> pdb=" O GLU D1000 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG D1005 " --> pdb=" O ALA D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1032 removed outlier: 4.203A pdb=" N LEU D1032 " --> pdb=" O ALA D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1036 through 1044 Processing helix chain 'D' and resid 1048 through 1067 removed outlier: 3.678A pdb=" N TYR D1052 " --> pdb=" O ASN D1048 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1094 removed outlier: 3.977A pdb=" N ILE D1077 " --> pdb=" O LEU D1073 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU D1085 " --> pdb=" O ILE D1081 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D1086 " --> pdb=" O LYS D1082 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER D1087 " --> pdb=" O ALA D1083 " (cutoff:3.500A) Processing helix chain 'D' and resid 1099 through 1122 removed outlier: 3.633A pdb=" N VAL D1103 " --> pdb=" O PRO D1099 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D1106 " --> pdb=" O TYR D1102 " (cutoff:3.500A) Proline residue: D1118 - end of helix Processing helix chain 'D' and resid 1126 through 1152 removed outlier: 3.588A pdb=" N LEU D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN D1152 " --> pdb=" O VAL D1148 " (cutoff:3.500A) Processing helix chain 'D' and resid 1162 through 1186 removed outlier: 3.996A pdb=" N TYR D1166 " --> pdb=" O PRO D1162 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS D1167 " --> pdb=" O LEU D1163 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D1168 " --> pdb=" O ASP D1164 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP D1179 " --> pdb=" O LEU D1175 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 98 removed outlier: 3.564A pdb=" N ILE E 88 " --> pdb=" O PHE E 84 " (cutoff:3.500A) Proline residue: E 95 - end of helix Processing helix chain 'E' and resid 112 through 141 removed outlier: 3.776A pdb=" N PHE E 116 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE E 127 " --> pdb=" O MET E 123 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE E 135 " --> pdb=" O GLY E 131 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 155 Processing helix chain 'E' and resid 157 through 179 removed outlier: 4.197A pdb=" N VAL E 161 " --> pdb=" O GLY E 157 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY E 177 " --> pdb=" O TYR E 173 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA E 178 " --> pdb=" O ILE E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 217 removed outlier: 3.803A pdb=" N MET E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 244 removed outlier: 3.984A pdb=" N MET E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 275 removed outlier: 5.938A pdb=" N ALA E 251 " --> pdb=" O TRP E 247 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE E 252 " --> pdb=" O MET E 248 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE E 253 " --> pdb=" O TRP E 249 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER E 255 " --> pdb=" O ALA E 251 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA E 256 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 312 removed outlier: 4.237A pdb=" N PHE E 310 " --> pdb=" O PHE E 306 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN E 311 " --> pdb=" O MET E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 346 removed outlier: 3.978A pdb=" N TRP E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR E 326 " --> pdb=" O GLN E 322 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR E 346 " --> pdb=" O ALA E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 384 removed outlier: 4.115A pdb=" N ALA E 352 " --> pdb=" O TRP E 348 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU E 360 " --> pdb=" O ARG E 356 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA E 361 " --> pdb=" O GLN E 357 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY E 362 " --> pdb=" O LYS E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 491 removed outlier: 4.322A pdb=" N GLU E 473 " --> pdb=" O ILE E 469 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU E 478 " --> pdb=" O ALA E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 495 Processing helix chain 'E' and resid 511 through 517 removed outlier: 3.806A pdb=" N PHE E 515 " --> pdb=" O ASP E 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 541 Processing helix chain 'E' and resid 544 through 555 removed outlier: 3.542A pdb=" N ALA E 548 " --> pdb=" O ASP E 544 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU E 549 " --> pdb=" O PRO E 545 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN E 550 " --> pdb=" O ARG E 546 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 578 removed outlier: 3.866A pdb=" N LEU E 562 " --> pdb=" O ASN E 558 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE E 563 " --> pdb=" O LEU E 559 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA E 564 " --> pdb=" O GLY E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 616 removed outlier: 4.376A pdb=" N MET E 602 " --> pdb=" O ALA E 598 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU E 603 " --> pdb=" O VAL E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 647 removed outlier: 3.697A pdb=" N VAL E 635 " --> pdb=" O ILE E 631 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA E 636 " --> pdb=" O VAL E 632 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA E 647 " --> pdb=" O TRP E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 652 through 677 removed outlier: 4.534A pdb=" N PHE E 656 " --> pdb=" O TRP E 652 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 657 " --> pdb=" O TYR E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 689 through 715 removed outlier: 3.728A pdb=" N CYS E 693 " --> pdb=" O SER E 689 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY E 706 " --> pdb=" O TRP E 702 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA E 715 " --> pdb=" O VAL E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 722 through 748 removed outlier: 3.696A pdb=" N LYS E 736 " --> pdb=" O ASP E 732 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR E 748 " --> pdb=" O MET E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 829 through 840 Processing helix chain 'E' and resid 846 through 853 removed outlier: 3.519A pdb=" N ARG E 850 " --> pdb=" O THR E 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 855 through 866 removed outlier: 3.614A pdb=" N LEU E 859 " --> pdb=" O ARG E 855 " (cutoff:3.500A) Processing helix chain 'E' and resid 879 through 893 removed outlier: 4.030A pdb=" N THR E 883 " --> pdb=" O TRP E 879 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG E 884 " --> pdb=" O GLU E 880 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS E 891 " --> pdb=" O THR E 887 " (cutoff:3.500A) Processing helix chain 'E' and resid 903 through 908 Processing helix chain 'E' and resid 918 through 937 removed outlier: 3.534A pdb=" N VAL E 922 " --> pdb=" O PHE E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 946 through 997 removed outlier: 3.673A pdb=" N HIS E 950 " --> pdb=" O SER E 946 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 952 " --> pdb=" O GLY E 948 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE E 953 " --> pdb=" O ILE E 949 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR E 965 " --> pdb=" O VAL E 961 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA E 968 " --> pdb=" O ARG E 964 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS E 970 " --> pdb=" O GLN E 966 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS E 971 " --> pdb=" O ALA E 967 " (cutoff:3.500A) Processing helix chain 'E' and resid 1000 through 1018 removed outlier: 3.791A pdb=" N ASN E1004 " --> pdb=" O GLU E1000 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG E1005 " --> pdb=" O ALA E1001 " (cutoff:3.500A) Processing helix chain 'E' and resid 1027 through 1032 removed outlier: 4.203A pdb=" N LEU E1032 " --> pdb=" O ALA E1029 " (cutoff:3.500A) Processing helix chain 'E' and resid 1036 through 1044 Processing helix chain 'E' and resid 1048 through 1067 removed outlier: 3.680A pdb=" N TYR E1052 " --> pdb=" O ASN E1048 " (cutoff:3.500A) Processing helix chain 'E' and resid 1073 through 1094 removed outlier: 3.977A pdb=" N ILE E1077 " --> pdb=" O LEU E1073 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU E1085 " --> pdb=" O ILE E1081 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN E1086 " --> pdb=" O LYS E1082 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER E1087 " --> pdb=" O ALA E1083 " (cutoff:3.500A) Processing helix chain 'E' and resid 1099 through 1122 removed outlier: 3.633A pdb=" N VAL E1103 " --> pdb=" O PRO E1099 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL E1106 " --> pdb=" O TYR E1102 " (cutoff:3.500A) Proline residue: E1118 - end of helix Processing helix chain 'E' and resid 1126 through 1152 removed outlier: 3.588A pdb=" N LEU E1130 " --> pdb=" O GLY E1126 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN E1152 " --> pdb=" O VAL E1148 " (cutoff:3.500A) Processing helix chain 'E' and resid 1162 through 1186 removed outlier: 3.996A pdb=" N TYR E1166 " --> pdb=" O PRO E1162 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS E1167 " --> pdb=" O LEU E1163 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E1168 " --> pdb=" O ASP E1164 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP E1179 " --> pdb=" O LEU E1175 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 584 through 585 Processing sheet with id=AA2, first strand: chain 'B' and resid 584 through 585 Processing sheet with id=AA3, first strand: chain 'C' and resid 584 through 585 Processing sheet with id=AA4, first strand: chain 'D' and resid 584 through 585 Processing sheet with id=AA5, first strand: chain 'E' and resid 584 through 585 2675 hydrogen bonds defined for protein. 7965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.69 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11752 1.34 - 1.46: 6783 1.46 - 1.57: 20085 1.57 - 1.69: 0 1.69 - 1.81: 375 Bond restraints: 38995 Sorted by residual: bond pdb=" N ARG E 877 " pdb=" CA ARG E 877 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.40e+00 bond pdb=" N ARG B 877 " pdb=" CA ARG B 877 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.36e+00 bond pdb=" N ARG C 877 " pdb=" CA ARG C 877 " ideal model delta sigma weight residual 1.455 1.486 -0.030 1.21e-02 6.83e+03 6.31e+00 bond pdb=" N ARG A 877 " pdb=" CA ARG A 877 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.21e-02 6.83e+03 6.06e+00 bond pdb=" N ARG D 877 " pdb=" CA ARG D 877 " ideal model delta sigma weight residual 1.455 1.485 -0.029 1.21e-02 6.83e+03 5.93e+00 ... (remaining 38990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 52455 2.12 - 4.24: 814 4.24 - 6.36: 71 6.36 - 8.48: 0 8.48 - 10.60: 20 Bond angle restraints: 53360 Sorted by residual: angle pdb=" N GLN B 721 " pdb=" CA GLN B 721 " pdb=" CB GLN B 721 " ideal model delta sigma weight residual 114.17 109.73 4.44 1.14e+00 7.69e-01 1.51e+01 angle pdb=" N GLN D 721 " pdb=" CA GLN D 721 " pdb=" CB GLN D 721 " ideal model delta sigma weight residual 114.17 109.77 4.40 1.14e+00 7.69e-01 1.49e+01 angle pdb=" N GLN A 721 " pdb=" CA GLN A 721 " pdb=" CB GLN A 721 " ideal model delta sigma weight residual 114.17 109.77 4.40 1.14e+00 7.69e-01 1.49e+01 angle pdb=" N GLN E 721 " pdb=" CA GLN E 721 " pdb=" CB GLN E 721 " ideal model delta sigma weight residual 114.17 109.77 4.40 1.14e+00 7.69e-01 1.49e+01 angle pdb=" N GLN C 721 " pdb=" CA GLN C 721 " pdb=" CB GLN C 721 " ideal model delta sigma weight residual 114.17 109.78 4.39 1.14e+00 7.69e-01 1.48e+01 ... (remaining 53355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 20225 17.60 - 35.20: 1715 35.20 - 52.80: 240 52.80 - 70.39: 45 70.39 - 87.99: 10 Dihedral angle restraints: 22235 sinusoidal: 7695 harmonic: 14540 Sorted by residual: dihedral pdb=" CA ARG C 385 " pdb=" C ARG C 385 " pdb=" N VAL C 386 " pdb=" CA VAL C 386 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ARG E 385 " pdb=" C ARG E 385 " pdb=" N VAL E 386 " pdb=" CA VAL E 386 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ARG A 385 " pdb=" C ARG A 385 " pdb=" N VAL A 386 " pdb=" CA VAL A 386 " ideal model delta harmonic sigma weight residual 180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 22232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 6165 0.338 - 0.676: 0 0.676 - 1.013: 0 1.013 - 1.351: 0 1.351 - 1.689: 10 Chirality restraints: 6175 Sorted by residual: chirality pdb=" CG LEU D 323 " pdb=" CB LEU D 323 " pdb=" CD1 LEU D 323 " pdb=" CD2 LEU D 323 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.13e+01 chirality pdb=" CG LEU E 323 " pdb=" CB LEU E 323 " pdb=" CD1 LEU E 323 " pdb=" CD2 LEU E 323 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.13e+01 chirality pdb=" CG LEU A 323 " pdb=" CB LEU A 323 " pdb=" CD1 LEU A 323 " pdb=" CD2 LEU A 323 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.13e+01 ... (remaining 6172 not shown) Planarity restraints: 6565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C1071 " -0.035 5.00e-02 4.00e+02 5.22e-02 4.37e+00 pdb=" N PRO C1072 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C1072 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C1072 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B1071 " -0.035 5.00e-02 4.00e+02 5.21e-02 4.35e+00 pdb=" N PRO B1072 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B1072 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B1072 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1071 " -0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A1072 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A1072 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1072 " -0.029 5.00e-02 4.00e+02 ... (remaining 6562 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5113 2.75 - 3.29: 40484 3.29 - 3.82: 62197 3.82 - 4.36: 66941 4.36 - 4.90: 117929 Nonbonded interactions: 292664 Sorted by model distance: nonbonded pdb=" OD1 ASP B 829 " pdb=" OG SER B 832 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASP E 829 " pdb=" OG SER E 832 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASP C 829 " pdb=" OG SER C 832 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASP A 829 " pdb=" OG SER A 832 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASP D 829 " pdb=" OG SER D 832 " model vdw 2.210 3.040 ... (remaining 292659 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.440 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 39000 Z= 0.247 Angle : 0.682 10.599 53360 Z= 0.398 Chirality : 0.079 1.689 6175 Planarity : 0.004 0.052 6565 Dihedral : 13.260 87.993 12815 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -3.28 (0.10), residues: 4930 helix: -1.64 (0.07), residues: 3475 sheet: None (None), residues: 0 loop : -3.20 (0.13), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1018 TYR 0.023 0.002 TYR D 637 PHE 0.019 0.001 PHE C1109 TRP 0.013 0.001 TRP C 520 HIS 0.005 0.001 HIS E1105 Details of bonding type rmsd covalent geometry : bond 0.00577 (38995) covalent geometry : angle 0.68232 (53360) hydrogen bonds : bond 0.12624 ( 2675) hydrogen bonds : angle 5.46599 ( 7965) Misc. bond : bond 0.00041 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 681 time to evaluate : 1.280 Fit side-chains REVERT: A 229 VAL cc_start: 0.8190 (m) cc_final: 0.7960 (p) REVERT: A 332 MET cc_start: 0.7217 (ttp) cc_final: 0.7014 (ttt) REVERT: A 627 PHE cc_start: 0.5705 (m-10) cc_final: 0.5119 (m-80) REVERT: E 263 LEU cc_start: 0.7557 (mt) cc_final: 0.7326 (mt) REVERT: E 332 MET cc_start: 0.7404 (ttp) cc_final: 0.7188 (ttt) REVERT: E 334 LEU cc_start: 0.8178 (mm) cc_final: 0.7960 (mt) outliers start: 0 outliers final: 0 residues processed: 681 average time/residue: 0.2019 time to fit residues: 233.0011 Evaluate side-chains 409 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 494 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 20.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 819 ASN B1004 ASN C1004 ASN D1004 ASN E 819 ASN E1004 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.168967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114605 restraints weight = 64825.191| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.21 r_work: 0.3233 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39000 Z= 0.148 Angle : 0.573 9.677 53360 Z= 0.305 Chirality : 0.040 0.160 6175 Planarity : 0.004 0.052 6565 Dihedral : 4.593 42.767 5375 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.24 % Allowed : 9.94 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.03 (0.11), residues: 4930 helix: 0.83 (0.08), residues: 3545 sheet: None (None), residues: 0 loop : -2.25 (0.15), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 835 TYR 0.027 0.002 TYR C 637 PHE 0.028 0.001 PHE B1109 TRP 0.021 0.001 TRP C 728 HIS 0.003 0.001 HIS E 682 Details of bonding type rmsd covalent geometry : bond 0.00308 (38995) covalent geometry : angle 0.57269 (53360) hydrogen bonds : bond 0.06158 ( 2675) hydrogen bonds : angle 3.88274 ( 7965) Misc. bond : bond 0.00058 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 487 time to evaluate : 1.150 Fit side-chains REVERT: A 123 MET cc_start: 0.8067 (tpt) cc_final: 0.7837 (tpp) REVERT: A 229 VAL cc_start: 0.8020 (m) cc_final: 0.7777 (p) REVERT: B 735 MET cc_start: 0.7659 (ttm) cc_final: 0.7388 (ttm) REVERT: B 864 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7736 (ttp80) REVERT: C 130 GLU cc_start: 0.7298 (mp0) cc_final: 0.6954 (mp0) REVERT: C 229 VAL cc_start: 0.8220 (m) cc_final: 0.8007 (p) REVERT: C 735 MET cc_start: 0.7486 (ttm) cc_final: 0.6909 (ttt) REVERT: D 71 ARG cc_start: 0.6509 (mmt180) cc_final: 0.6275 (mtt-85) REVERT: D 523 MET cc_start: 0.7412 (tpp) cc_final: 0.7064 (tpp) REVERT: D 735 MET cc_start: 0.8158 (ttt) cc_final: 0.7874 (tmm) REVERT: E 130 GLU cc_start: 0.7306 (mp0) cc_final: 0.6997 (mp0) REVERT: E 263 LEU cc_start: 0.8121 (mt) cc_final: 0.7735 (mp) REVERT: E 735 MET cc_start: 0.7098 (ttm) cc_final: 0.6871 (ttt) outliers start: 45 outliers final: 27 residues processed: 513 average time/residue: 0.1835 time to fit residues: 163.4473 Evaluate side-chains 426 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 399 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 652 TRP Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 863 LYS Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 739 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 103 optimal weight: 50.0000 chunk 35 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 465 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 264 optimal weight: 2.9990 chunk 378 optimal weight: 0.8980 chunk 170 optimal weight: 0.3980 chunk 234 optimal weight: 20.0000 chunk 193 optimal weight: 0.8980 chunk 319 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 ASN A 558 ASN B 558 ASN B1004 ASN C 558 ASN C1004 ASN D 558 ASN D1004 ASN E 336 HIS E 550 ASN E 558 ASN E1004 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.170878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118008 restraints weight = 65281.203| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.30 r_work: 0.3273 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 39000 Z= 0.116 Angle : 0.499 8.032 53360 Z= 0.265 Chirality : 0.037 0.140 6175 Planarity : 0.004 0.049 6565 Dihedral : 4.180 35.817 5375 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.87 % Allowed : 12.73 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.38 (0.12), residues: 4930 helix: 1.90 (0.09), residues: 3540 sheet: None (None), residues: 0 loop : -1.76 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 835 TYR 0.025 0.001 TYR A 637 PHE 0.031 0.001 PHE C1109 TRP 0.017 0.001 TRP C 728 HIS 0.002 0.000 HIS D 518 Details of bonding type rmsd covalent geometry : bond 0.00230 (38995) covalent geometry : angle 0.49881 (53360) hydrogen bonds : bond 0.05005 ( 2675) hydrogen bonds : angle 3.50348 ( 7965) Misc. bond : bond 0.00011 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 484 time to evaluate : 1.140 Fit side-chains REVERT: A 123 MET cc_start: 0.8055 (tpt) cc_final: 0.7770 (tpp) REVERT: A 229 VAL cc_start: 0.8113 (m) cc_final: 0.7910 (p) REVERT: A 835 ARG cc_start: 0.8569 (mtp85) cc_final: 0.8235 (ttm-80) REVERT: B 638 MET cc_start: 0.7277 (tpp) cc_final: 0.6816 (tpp) REVERT: B 735 MET cc_start: 0.7668 (ttm) cc_final: 0.7444 (ttm) REVERT: B 861 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7384 (tp30) REVERT: B 864 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7648 (ttp80) REVERT: C 123 MET cc_start: 0.7864 (tpp) cc_final: 0.7432 (mmm) REVERT: C 735 MET cc_start: 0.7317 (ttm) cc_final: 0.6641 (ttt) REVERT: D 130 GLU cc_start: 0.7178 (mp0) cc_final: 0.6966 (mp0) REVERT: D 523 MET cc_start: 0.7374 (tpp) cc_final: 0.6978 (tpp) REVERT: D 735 MET cc_start: 0.8079 (ttt) cc_final: 0.7832 (tmm) REVERT: E 263 LEU cc_start: 0.8100 (mt) cc_final: 0.7715 (mp) REVERT: E 307 MET cc_start: 0.7165 (ttp) cc_final: 0.6937 (tmm) REVERT: E 735 MET cc_start: 0.7084 (ttm) cc_final: 0.6795 (tmm) REVERT: E 1129 MET cc_start: 0.7401 (ppp) cc_final: 0.7198 (ppp) outliers start: 68 outliers final: 37 residues processed: 527 average time/residue: 0.1854 time to fit residues: 169.0307 Evaluate side-chains 438 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 401 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain B residue 268 TYR Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 985 MET Chi-restraints excluded: chain C residue 268 TYR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 652 TRP Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 893 ILE Chi-restraints excluded: chain E residue 120 TRP Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 893 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 202 optimal weight: 50.0000 chunk 351 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 359 optimal weight: 8.9990 chunk 329 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 369 optimal weight: 0.3980 chunk 232 optimal weight: 10.0000 chunk 415 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1023 ASN C1004 ASN C1023 ASN D1023 ASN E 752 ASN E1023 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.163114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105261 restraints weight = 65249.785| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.11 r_work: 0.3126 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 39000 Z= 0.215 Angle : 0.620 13.079 53360 Z= 0.328 Chirality : 0.042 0.199 6175 Planarity : 0.004 0.052 6565 Dihedral : 4.408 23.874 5375 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.67 % Allowed : 15.76 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.12 (0.12), residues: 4930 helix: 1.68 (0.09), residues: 3605 sheet: None (None), residues: 0 loop : -1.96 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 835 TYR 0.020 0.002 TYR B 234 PHE 0.037 0.002 PHE B1109 TRP 0.026 0.001 TRP C 728 HIS 0.004 0.001 HIS A 849 Details of bonding type rmsd covalent geometry : bond 0.00509 (38995) covalent geometry : angle 0.62034 (53360) hydrogen bonds : bond 0.07717 ( 2675) hydrogen bonds : angle 3.82704 ( 7965) Misc. bond : bond 0.00053 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 442 time to evaluate : 1.333 Fit side-chains REVERT: A 123 MET cc_start: 0.8241 (tpt) cc_final: 0.7933 (tpp) REVERT: A 229 VAL cc_start: 0.8118 (m) cc_final: 0.7916 (p) REVERT: A 381 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6713 (ttm170) REVERT: A 653 TYR cc_start: 0.6950 (OUTLIER) cc_final: 0.5361 (t80) REVERT: A 941 PHE cc_start: 0.5536 (t80) cc_final: 0.5308 (t80) REVERT: B 653 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.6324 (t80) REVERT: B 735 MET cc_start: 0.7733 (ttm) cc_final: 0.7413 (ttm) REVERT: C 123 MET cc_start: 0.7961 (tpp) cc_final: 0.7539 (mmm) REVERT: C 130 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6804 (mp0) REVERT: C 735 MET cc_start: 0.7447 (ttm) cc_final: 0.6895 (ttm) REVERT: D 130 GLU cc_start: 0.7222 (mp0) cc_final: 0.6954 (mp0) REVERT: D 523 MET cc_start: 0.7467 (tpp) cc_final: 0.7061 (tpp) REVERT: D 611 LEU cc_start: 0.7749 (mt) cc_final: 0.7481 (mt) REVERT: D 735 MET cc_start: 0.8203 (ttt) cc_final: 0.7914 (tmm) REVERT: E 130 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7104 (mp0) REVERT: E 307 MET cc_start: 0.7258 (ttp) cc_final: 0.6972 (tmm) REVERT: E 653 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.5577 (t80) outliers start: 97 outliers final: 62 residues processed: 510 average time/residue: 0.1817 time to fit residues: 163.5782 Evaluate side-chains 465 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 399 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 268 TYR Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 268 TYR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 652 TRP Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 732 ASP Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 893 ILE Chi-restraints excluded: chain E residue 120 TRP Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 653 TYR Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 842 GLN Chi-restraints excluded: chain E residue 893 ILE Chi-restraints excluded: chain E residue 1087 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 9 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 372 optimal weight: 9.9990 chunk 467 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 326 optimal weight: 9.9990 chunk 303 optimal weight: 1.9990 chunk 351 optimal weight: 0.0010 chunk 183 optimal weight: 0.9980 chunk 320 optimal weight: 5.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 739 HIS B1004 ASN C1004 ASN D1004 ASN E 375 HIS E1004 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.166755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110937 restraints weight = 65223.548| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.20 r_work: 0.3191 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 39000 Z= 0.127 Angle : 0.523 11.745 53360 Z= 0.273 Chirality : 0.038 0.159 6175 Planarity : 0.004 0.051 6565 Dihedral : 4.133 28.815 5375 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.56 % Allowed : 17.27 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.63 (0.12), residues: 4930 helix: 2.08 (0.09), residues: 3565 sheet: None (None), residues: 0 loop : -1.73 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1093 TYR 0.022 0.001 TYR D 637 PHE 0.036 0.001 PHE C1109 TRP 0.020 0.001 TRP C 728 HIS 0.002 0.000 HIS A1020 Details of bonding type rmsd covalent geometry : bond 0.00263 (38995) covalent geometry : angle 0.52320 (53360) hydrogen bonds : bond 0.05643 ( 2675) hydrogen bonds : angle 3.49924 ( 7965) Misc. bond : bond 0.00035 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 452 time to evaluate : 1.348 Fit side-chains REVERT: A 123 MET cc_start: 0.8195 (tpt) cc_final: 0.7897 (tpp) REVERT: A 229 VAL cc_start: 0.8079 (m) cc_final: 0.7876 (p) REVERT: A 381 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6616 (ttm170) REVERT: B 307 MET cc_start: 0.7015 (ttp) cc_final: 0.6803 (tmm) REVERT: B 381 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6685 (ttm170) REVERT: B 653 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.6269 (t80) REVERT: B 735 MET cc_start: 0.7781 (ttm) cc_final: 0.7298 (ttm) REVERT: B 864 ARG cc_start: 0.8225 (ttp-110) cc_final: 0.7985 (ttp80) REVERT: B 1063 GLU cc_start: 0.8979 (tt0) cc_final: 0.8634 (tt0) REVERT: C 123 MET cc_start: 0.7894 (tpp) cc_final: 0.7454 (mmm) REVERT: C 307 MET cc_start: 0.7233 (ttp) cc_final: 0.7022 (tmm) REVERT: C 381 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6715 (ttm170) REVERT: C 638 MET cc_start: 0.7283 (tpp) cc_final: 0.6664 (tpp) REVERT: D 381 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6726 (ttm170) REVERT: D 523 MET cc_start: 0.7378 (tpp) cc_final: 0.6948 (tpp) REVERT: D 607 ASP cc_start: 0.5597 (t70) cc_final: 0.5323 (t0) REVERT: D 611 LEU cc_start: 0.7785 (mt) cc_final: 0.7492 (mt) REVERT: D 735 MET cc_start: 0.8157 (ttt) cc_final: 0.7827 (tmm) REVERT: E 130 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6922 (mp0) REVERT: E 263 LEU cc_start: 0.8051 (mt) cc_final: 0.7743 (mp) REVERT: E 307 MET cc_start: 0.7209 (ttp) cc_final: 0.6987 (tmm) REVERT: E 381 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6680 (ttm170) REVERT: E 653 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.5738 (t80) REVERT: E 735 MET cc_start: 0.7206 (ttm) cc_final: 0.6702 (tmm) REVERT: E 853 MET cc_start: 0.8736 (ptp) cc_final: 0.8521 (ptp) outliers start: 93 outliers final: 66 residues processed: 519 average time/residue: 0.1799 time to fit residues: 162.3494 Evaluate side-chains 476 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 403 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 268 TYR Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 268 TYR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1120 ILE Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 893 ILE Chi-restraints excluded: chain D residue 1112 ILE Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain E residue 120 TRP Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 381 ARG Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 653 TYR Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 842 GLN Chi-restraints excluded: chain E residue 893 ILE Chi-restraints excluded: chain E residue 1112 ILE Chi-restraints excluded: chain E residue 1120 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 328 optimal weight: 6.9990 chunk 321 optimal weight: 9.9990 chunk 239 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 420 optimal weight: 8.9990 chunk 343 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 375 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 5 optimal weight: 20.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 550 ASN E1004 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.163103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106200 restraints weight = 65179.288| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.18 r_work: 0.3131 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 39000 Z= 0.192 Angle : 0.596 14.267 53360 Z= 0.312 Chirality : 0.041 0.178 6175 Planarity : 0.004 0.053 6565 Dihedral : 4.297 25.225 5375 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.09 % Allowed : 17.22 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.45 (0.12), residues: 4930 helix: 1.93 (0.08), residues: 3585 sheet: None (None), residues: 0 loop : -1.80 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 976 TYR 0.021 0.002 TYR D 578 PHE 0.039 0.002 PHE C1109 TRP 0.025 0.001 TRP C 728 HIS 0.003 0.001 HIS C 849 Details of bonding type rmsd covalent geometry : bond 0.00450 (38995) covalent geometry : angle 0.59556 (53360) hydrogen bonds : bond 0.07306 ( 2675) hydrogen bonds : angle 3.69350 ( 7965) Misc. bond : bond 0.00085 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 416 time to evaluate : 1.332 Fit side-chains REVERT: A 123 MET cc_start: 0.8313 (tpt) cc_final: 0.8085 (tpp) REVERT: A 229 VAL cc_start: 0.8070 (m) cc_final: 0.7867 (p) REVERT: A 381 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6728 (ttm170) REVERT: A 653 TYR cc_start: 0.6955 (OUTLIER) cc_final: 0.5397 (t80) REVERT: B 176 MET cc_start: 0.6533 (mmm) cc_final: 0.6152 (mmm) REVERT: B 200 GLU cc_start: 0.5860 (OUTLIER) cc_final: 0.5548 (pp20) REVERT: B 307 MET cc_start: 0.7042 (ttp) cc_final: 0.6805 (tmm) REVERT: B 381 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6768 (ttm170) REVERT: B 653 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.6312 (t80) REVERT: B 735 MET cc_start: 0.7757 (ttm) cc_final: 0.7284 (ttm) REVERT: B 859 LEU cc_start: 0.7583 (tp) cc_final: 0.7344 (tt) REVERT: B 870 PHE cc_start: 0.7272 (m-80) cc_final: 0.7049 (m-80) REVERT: B 1063 GLU cc_start: 0.8972 (tt0) cc_final: 0.8627 (tt0) REVERT: C 123 MET cc_start: 0.7961 (tpp) cc_final: 0.7539 (mmm) REVERT: C 130 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6848 (mp0) REVERT: C 307 MET cc_start: 0.7314 (ttp) cc_final: 0.7060 (tmm) REVERT: C 381 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6776 (ttm170) REVERT: D 130 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6861 (mp0) REVERT: D 381 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6810 (ttm170) REVERT: D 523 MET cc_start: 0.7532 (tpp) cc_final: 0.7115 (tpp) REVERT: D 735 MET cc_start: 0.8187 (ttt) cc_final: 0.7881 (tmm) REVERT: D 847 ASP cc_start: 0.7886 (m-30) cc_final: 0.7549 (t0) REVERT: E 130 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6961 (mp0) REVERT: E 307 MET cc_start: 0.7263 (ttp) cc_final: 0.7029 (tmm) REVERT: E 381 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6726 (ttm170) REVERT: E 638 MET cc_start: 0.7238 (tpp) cc_final: 0.6988 (tpp) REVERT: E 653 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.5762 (t80) outliers start: 112 outliers final: 87 residues processed: 506 average time/residue: 0.1807 time to fit residues: 159.2191 Evaluate side-chains 487 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 391 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 705 TYR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1183 SER Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 268 TYR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1120 ILE Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 893 ILE Chi-restraints excluded: chain D residue 1087 SER Chi-restraints excluded: chain D residue 1112 ILE Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain E residue 120 TRP Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 381 ARG Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 586 VAL Chi-restraints excluded: chain E residue 653 TYR Chi-restraints excluded: chain E residue 705 TYR Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 842 GLN Chi-restraints excluded: chain E residue 893 ILE Chi-restraints excluded: chain E residue 904 MET Chi-restraints excluded: chain E residue 1087 SER Chi-restraints excluded: chain E residue 1112 ILE Chi-restraints excluded: chain E residue 1120 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 269 optimal weight: 0.0980 chunk 4 optimal weight: 50.0000 chunk 60 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 57 optimal weight: 0.1980 chunk 443 optimal weight: 0.9980 chunk 467 optimal weight: 7.9990 chunk 463 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1004 ASN E 550 ASN E1004 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.166414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.110203 restraints weight = 65499.893| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.11 r_work: 0.3196 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 39000 Z= 0.133 Angle : 0.542 14.790 53360 Z= 0.278 Chirality : 0.038 0.173 6175 Planarity : 0.004 0.055 6565 Dihedral : 4.104 27.326 5375 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.89 % Allowed : 17.99 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.81 (0.12), residues: 4930 helix: 2.20 (0.08), residues: 3540 sheet: None (None), residues: 0 loop : -1.58 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1093 TYR 0.021 0.001 TYR E 637 PHE 0.036 0.001 PHE A1109 TRP 0.017 0.001 TRP B 728 HIS 0.002 0.000 HIS E 849 Details of bonding type rmsd covalent geometry : bond 0.00288 (38995) covalent geometry : angle 0.54174 (53360) hydrogen bonds : bond 0.05862 ( 2675) hydrogen bonds : angle 3.50258 ( 7965) Misc. bond : bond 0.00057 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 426 time to evaluate : 0.954 Fit side-chains REVERT: A 123 MET cc_start: 0.8264 (tpt) cc_final: 0.8060 (tpp) REVERT: A 229 VAL cc_start: 0.7955 (m) cc_final: 0.7742 (p) REVERT: A 381 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6686 (ttm170) REVERT: A 653 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.5328 (t80) REVERT: B 200 GLU cc_start: 0.5701 (OUTLIER) cc_final: 0.5448 (pp20) REVERT: B 307 MET cc_start: 0.6980 (ttp) cc_final: 0.6761 (tmm) REVERT: B 381 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6704 (ttm170) REVERT: B 653 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.6085 (t80) REVERT: B 735 MET cc_start: 0.7769 (ttm) cc_final: 0.7238 (ttm) REVERT: B 1063 GLU cc_start: 0.8958 (tt0) cc_final: 0.8568 (tt0) REVERT: C 123 MET cc_start: 0.7856 (tpp) cc_final: 0.7450 (mmm) REVERT: C 307 MET cc_start: 0.7195 (ttp) cc_final: 0.6988 (tmm) REVERT: C 381 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6752 (ttm170) REVERT: C 638 MET cc_start: 0.7286 (tpp) cc_final: 0.6654 (tpp) REVERT: D 381 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6741 (ttm170) REVERT: D 523 MET cc_start: 0.7347 (tpp) cc_final: 0.6941 (tpp) REVERT: D 735 MET cc_start: 0.8097 (ttt) cc_final: 0.7773 (tmm) REVERT: E 263 LEU cc_start: 0.8080 (mt) cc_final: 0.7806 (mp) REVERT: E 381 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6768 (ttm170) REVERT: E 638 MET cc_start: 0.7147 (tpp) cc_final: 0.6842 (tpp) REVERT: E 653 TYR cc_start: 0.6777 (OUTLIER) cc_final: 0.5655 (t80) REVERT: E 735 MET cc_start: 0.7119 (ttm) cc_final: 0.6533 (tmm) outliers start: 105 outliers final: 87 residues processed: 507 average time/residue: 0.1871 time to fit residues: 164.4775 Evaluate side-chains 501 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 405 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 268 TYR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1120 ILE Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 705 TYR Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 893 ILE Chi-restraints excluded: chain D residue 1087 SER Chi-restraints excluded: chain D residue 1112 ILE Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain E residue 120 TRP Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 381 ARG Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 586 VAL Chi-restraints excluded: chain E residue 653 TYR Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 705 TYR Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 842 GLN Chi-restraints excluded: chain E residue 893 ILE Chi-restraints excluded: chain E residue 904 MET Chi-restraints excluded: chain E residue 1087 SER Chi-restraints excluded: chain E residue 1112 ILE Chi-restraints excluded: chain E residue 1120 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 79 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 446 optimal weight: 6.9990 chunk 410 optimal weight: 6.9990 chunk 309 optimal weight: 50.0000 chunk 103 optimal weight: 40.0000 chunk 180 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 333 optimal weight: 20.0000 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1004 ASN E 550 ASN E1004 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.164590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107960 restraints weight = 65371.217| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.13 r_work: 0.3160 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 39000 Z= 0.164 Angle : 0.571 14.869 53360 Z= 0.296 Chirality : 0.039 0.172 6175 Planarity : 0.004 0.054 6565 Dihedral : 4.151 25.499 5375 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.33 % Allowed : 18.10 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.74 (0.12), residues: 4930 helix: 2.15 (0.08), residues: 3545 sheet: None (None), residues: 0 loop : -1.62 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 976 TYR 0.021 0.001 TYR D 578 PHE 0.037 0.001 PHE C1109 TRP 0.021 0.001 TRP E 728 HIS 0.002 0.001 HIS E 849 Details of bonding type rmsd covalent geometry : bond 0.00376 (38995) covalent geometry : angle 0.57094 (53360) hydrogen bonds : bond 0.06672 ( 2675) hydrogen bonds : angle 3.59353 ( 7965) Misc. bond : bond 0.00066 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 412 time to evaluate : 1.201 Fit side-chains REVERT: A 123 MET cc_start: 0.8231 (tpt) cc_final: 0.8004 (tpp) REVERT: A 229 VAL cc_start: 0.7958 (m) cc_final: 0.7756 (p) REVERT: A 381 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6626 (ttm170) REVERT: A 653 TYR cc_start: 0.6733 (OUTLIER) cc_final: 0.5305 (t80) REVERT: B 123 MET cc_start: 0.7854 (tpp) cc_final: 0.7279 (mmm) REVERT: B 200 GLU cc_start: 0.5701 (OUTLIER) cc_final: 0.5428 (pp20) REVERT: B 307 MET cc_start: 0.6969 (ttp) cc_final: 0.6758 (tmm) REVERT: B 381 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6724 (ttm170) REVERT: B 653 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.5998 (t80) REVERT: B 735 MET cc_start: 0.7748 (ttm) cc_final: 0.7258 (ttm) REVERT: B 859 LEU cc_start: 0.7509 (tp) cc_final: 0.7284 (tt) REVERT: B 1063 GLU cc_start: 0.8980 (tt0) cc_final: 0.8600 (tt0) REVERT: C 123 MET cc_start: 0.7883 (tpp) cc_final: 0.7462 (mmm) REVERT: C 130 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6734 (mp0) REVERT: C 307 MET cc_start: 0.7239 (ttp) cc_final: 0.7029 (tmm) REVERT: C 381 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6749 (ttm170) REVERT: D 130 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6726 (mm-30) REVERT: D 234 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.6898 (p90) REVERT: D 381 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6718 (ttm170) REVERT: D 523 MET cc_start: 0.7417 (tpp) cc_final: 0.7031 (tpp) REVERT: D 735 MET cc_start: 0.8127 (ttt) cc_final: 0.7825 (tmm) REVERT: E 263 LEU cc_start: 0.8088 (mt) cc_final: 0.7812 (mp) REVERT: E 381 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6710 (ttm170) REVERT: E 638 MET cc_start: 0.7153 (tpp) cc_final: 0.6901 (tpp) REVERT: E 653 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.5791 (t80) outliers start: 121 outliers final: 105 residues processed: 510 average time/residue: 0.1850 time to fit residues: 164.0429 Evaluate side-chains 516 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 401 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 705 TYR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 705 TYR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 268 TYR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 732 ASP Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1120 ILE Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 302 TYR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 705 TYR Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 893 ILE Chi-restraints excluded: chain D residue 1087 SER Chi-restraints excluded: chain D residue 1112 ILE Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain D residue 1183 SER Chi-restraints excluded: chain E residue 120 TRP Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 381 ARG Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 586 VAL Chi-restraints excluded: chain E residue 653 TYR Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 705 TYR Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 842 GLN Chi-restraints excluded: chain E residue 893 ILE Chi-restraints excluded: chain E residue 904 MET Chi-restraints excluded: chain E residue 1087 SER Chi-restraints excluded: chain E residue 1112 ILE Chi-restraints excluded: chain E residue 1120 ILE Chi-restraints excluded: chain E residue 1183 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 60 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 313 optimal weight: 6.9990 chunk 189 optimal weight: 0.1980 chunk 481 optimal weight: 0.7980 chunk 470 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 171 optimal weight: 20.0000 chunk 413 optimal weight: 20.0000 chunk 322 optimal weight: 0.0470 chunk 364 optimal weight: 2.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1004 ASN E1004 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.167528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111496 restraints weight = 65956.910| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.17 r_work: 0.3224 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 39000 Z= 0.119 Angle : 0.526 15.505 53360 Z= 0.269 Chirality : 0.038 0.182 6175 Planarity : 0.004 0.054 6565 Dihedral : 3.963 28.088 5375 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.33 % Allowed : 18.07 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.97 (0.12), residues: 4930 helix: 2.32 (0.08), residues: 3540 sheet: None (None), residues: 0 loop : -1.51 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1093 TYR 0.022 0.001 TYR E 637 PHE 0.035 0.001 PHE A1109 TRP 0.018 0.001 TRP E 728 HIS 0.002 0.000 HIS C1105 Details of bonding type rmsd covalent geometry : bond 0.00249 (38995) covalent geometry : angle 0.52580 (53360) hydrogen bonds : bond 0.05323 ( 2675) hydrogen bonds : angle 3.42434 ( 7965) Misc. bond : bond 0.00052 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 439 time to evaluate : 1.336 Fit side-chains REVERT: A 123 MET cc_start: 0.8128 (tpt) cc_final: 0.7827 (tpp) REVERT: A 229 VAL cc_start: 0.7995 (m) cc_final: 0.7786 (p) REVERT: A 258 TRP cc_start: 0.6251 (m100) cc_final: 0.6029 (m100) REVERT: A 381 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6670 (ttm170) REVERT: A 653 TYR cc_start: 0.6721 (OUTLIER) cc_final: 0.5341 (t80) REVERT: A 879 TRP cc_start: 0.5264 (m-10) cc_final: 0.5009 (m-10) REVERT: B 123 MET cc_start: 0.7767 (tpp) cc_final: 0.7209 (mmm) REVERT: B 200 GLU cc_start: 0.5554 (OUTLIER) cc_final: 0.5298 (pp20) REVERT: B 381 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6523 (ttm170) REVERT: B 653 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.5691 (t80) REVERT: B 735 MET cc_start: 0.7717 (ttm) cc_final: 0.7163 (ttm) REVERT: B 1063 GLU cc_start: 0.8912 (tt0) cc_final: 0.8508 (tt0) REVERT: C 123 MET cc_start: 0.7859 (tpp) cc_final: 0.7452 (mmm) REVERT: C 368 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6743 (mp) REVERT: C 381 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6690 (ttm170) REVERT: C 523 MET cc_start: 0.7542 (mmp) cc_final: 0.7167 (mmp) REVERT: C 853 MET cc_start: 0.8733 (ptp) cc_final: 0.8524 (ptp) REVERT: C 879 TRP cc_start: 0.5243 (m-10) cc_final: 0.4976 (m-90) REVERT: D 130 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6530 (mm-30) REVERT: D 381 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6615 (ttm170) REVERT: D 523 MET cc_start: 0.7313 (tpp) cc_final: 0.6934 (tpp) REVERT: D 735 MET cc_start: 0.8090 (ttt) cc_final: 0.7773 (tmm) REVERT: E 123 MET cc_start: 0.7785 (tpp) cc_final: 0.7203 (mmm) REVERT: E 263 LEU cc_start: 0.8086 (mt) cc_final: 0.7812 (mp) REVERT: E 381 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6580 (ttm170) REVERT: E 638 MET cc_start: 0.7092 (tpp) cc_final: 0.6783 (tpp) REVERT: E 653 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.5810 (t80) REVERT: E 879 TRP cc_start: 0.5216 (m-90) cc_final: 0.5010 (m-90) outliers start: 121 outliers final: 94 residues processed: 535 average time/residue: 0.1825 time to fit residues: 168.7099 Evaluate side-chains 519 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 415 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 705 TYR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 268 TYR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1120 ILE Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 302 TYR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 893 ILE Chi-restraints excluded: chain D residue 1087 SER Chi-restraints excluded: chain D residue 1112 ILE Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain E residue 120 TRP Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 381 ARG Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 586 VAL Chi-restraints excluded: chain E residue 653 TYR Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 705 TYR Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 842 GLN Chi-restraints excluded: chain E residue 893 ILE Chi-restraints excluded: chain E residue 1087 SER Chi-restraints excluded: chain E residue 1120 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 132 optimal weight: 10.0000 chunk 397 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 421 optimal weight: 3.9990 chunk 431 optimal weight: 8.9990 chunk 453 optimal weight: 20.0000 chunk 182 optimal weight: 0.6980 chunk 470 optimal weight: 0.8980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1004 ASN E1004 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.163410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.105067 restraints weight = 65576.981| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.94 r_work: 0.3157 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 39000 Z= 0.198 Angle : 0.612 14.843 53360 Z= 0.317 Chirality : 0.041 0.193 6175 Planarity : 0.004 0.053 6565 Dihedral : 4.204 25.685 5375 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.06 % Allowed : 18.60 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.70 (0.12), residues: 4930 helix: 2.12 (0.08), residues: 3540 sheet: None (None), residues: 0 loop : -1.61 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 372 TYR 0.023 0.002 TYR D 578 PHE 0.038 0.001 PHE C1109 TRP 0.024 0.001 TRP B 728 HIS 0.003 0.001 HIS C 849 Details of bonding type rmsd covalent geometry : bond 0.00468 (38995) covalent geometry : angle 0.61171 (53360) hydrogen bonds : bond 0.07243 ( 2675) hydrogen bonds : angle 3.68904 ( 7965) Misc. bond : bond 0.00083 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 424 time to evaluate : 1.373 Fit side-chains REVERT: A 123 MET cc_start: 0.8218 (tpt) cc_final: 0.7987 (tpp) REVERT: A 258 TRP cc_start: 0.6289 (m100) cc_final: 0.6059 (m100) REVERT: A 381 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6681 (ttm170) REVERT: A 653 TYR cc_start: 0.6787 (OUTLIER) cc_final: 0.5406 (t80) REVERT: B 123 MET cc_start: 0.7842 (tpp) cc_final: 0.7262 (mmm) REVERT: B 200 GLU cc_start: 0.5737 (OUTLIER) cc_final: 0.5462 (pp20) REVERT: B 381 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6832 (ttm170) REVERT: B 653 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.5659 (t80) REVERT: B 735 MET cc_start: 0.7730 (ttm) cc_final: 0.7238 (ttm) REVERT: B 859 LEU cc_start: 0.7548 (tp) cc_final: 0.7323 (tt) REVERT: B 1063 GLU cc_start: 0.8903 (tt0) cc_final: 0.8526 (tt0) REVERT: C 123 MET cc_start: 0.7918 (tpp) cc_final: 0.7513 (mmm) REVERT: C 130 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6676 (mp0) REVERT: C 381 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6833 (ttm170) REVERT: C 879 TRP cc_start: 0.5416 (m-10) cc_final: 0.5160 (m-90) REVERT: D 130 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6528 (mm-30) REVERT: D 381 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6819 (ttm170) REVERT: D 523 MET cc_start: 0.7372 (tpp) cc_final: 0.6974 (tpp) REVERT: D 735 MET cc_start: 0.8108 (ttt) cc_final: 0.7808 (tmm) REVERT: E 381 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6757 (ttm170) REVERT: E 653 TYR cc_start: 0.6918 (OUTLIER) cc_final: 0.5878 (t80) REVERT: E 735 MET cc_start: 0.7227 (ttm) cc_final: 0.6878 (ttm) REVERT: E 1063 GLU cc_start: 0.8819 (tt0) cc_final: 0.8418 (tt0) outliers start: 111 outliers final: 94 residues processed: 512 average time/residue: 0.1839 time to fit residues: 163.1939 Evaluate side-chains 512 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 409 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 705 TYR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 268 TYR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1120 ILE Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain D residue 705 TYR Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 893 ILE Chi-restraints excluded: chain D residue 1112 ILE Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain E residue 120 TRP Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 381 ARG Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 586 VAL Chi-restraints excluded: chain E residue 653 TYR Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 705 TYR Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 842 GLN Chi-restraints excluded: chain E residue 893 ILE Chi-restraints excluded: chain E residue 904 MET Chi-restraints excluded: chain E residue 1087 SER Chi-restraints excluded: chain E residue 1112 ILE Chi-restraints excluded: chain E residue 1120 ILE Chi-restraints excluded: chain E residue 1183 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 19 optimal weight: 6.9990 chunk 490 optimal weight: 0.8980 chunk 296 optimal weight: 0.7980 chunk 238 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 159 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 379 optimal weight: 0.4980 chunk 453 optimal weight: 20.0000 chunk 28 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1004 ASN C1149 GLN E1004 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.169862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115854 restraints weight = 65335.252| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.13 r_work: 0.3277 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 39000 Z= 0.109 Angle : 0.526 15.681 53360 Z= 0.265 Chirality : 0.038 0.187 6175 Planarity : 0.004 0.055 6565 Dihedral : 3.904 34.333 5375 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.37 % Allowed : 19.59 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.08 (0.12), residues: 4930 helix: 2.45 (0.08), residues: 3505 sheet: None (None), residues: 0 loop : -1.50 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 372 TYR 0.025 0.001 TYR E 637 PHE 0.028 0.001 PHE C1109 TRP 0.016 0.001 TRP B1127 HIS 0.003 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00217 (38995) covalent geometry : angle 0.52564 (53360) hydrogen bonds : bond 0.04546 ( 2675) hydrogen bonds : angle 3.36476 ( 7965) Misc. bond : bond 0.00052 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14373.04 seconds wall clock time: 244 minutes 20.74 seconds (14660.74 seconds total)