Starting phenix.real_space_refine on Tue Nov 19 15:49:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5t_17452/11_2024/8p5t_17452.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5t_17452/11_2024/8p5t_17452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5t_17452/11_2024/8p5t_17452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5t_17452/11_2024/8p5t_17452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5t_17452/11_2024/8p5t_17452.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5t_17452/11_2024/8p5t_17452.cif" } resolution = 2.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.018 sd= 1.217 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: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 6 5.21 5 S 228 5.16 5 C 32994 2.51 5 N 9228 2.21 5 O 10104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 160 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 52590 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' MG': 1, 'ACO': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' MG': 1, 'ACO': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' MG': 1, 'ACO': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' MG': 1, 'ACO': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' MG': 1, 'ACO': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' MG': 1, 'ACO': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 26.51, per 1000 atoms: 0.50 Number of scatterers: 52590 At special positions: 0 Unit cell: (227.9, 209.84, 171.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 228 16.00 P 30 15.00 Mg 6 11.99 O 10104 8.00 N 9228 7.00 C 32994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.22 Conformation dependent library (CDL) restraints added in 6.2 seconds 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12252 Finding SS restraints... Secondary structure from input PDB file: 300 helices and 42 sheets defined 49.2% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.51 Creating SS restraints... Processing helix chain 'A' and resid 109 through 121 Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 135 through 152 Processing helix chain 'A' and resid 158 through 174 removed outlier: 3.596A pdb=" N ILE A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 225 through 243 Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 288 through 292 removed outlier: 3.704A pdb=" N GLN A 292 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 320 through 335 Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.551A pdb=" N TRP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 384 through 387 removed outlier: 3.605A pdb=" N ALA A 387 " --> pdb=" O HIS A 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.840A pdb=" N LEU A 407 " --> pdb=" O HIS A 404 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 427 through 431 Processing helix chain 'A' and resid 436 through 448 Processing helix chain 'A' and resid 460 through 474 removed outlier: 3.678A pdb=" N GLY A 474 " --> pdb=" O ARG A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 504 Processing helix chain 'A' and resid 517 through 533 Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 557 through 566 removed outlier: 3.814A pdb=" N ILE A 561 " --> pdb=" O PRO A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 removed outlier: 3.924A pdb=" N LEU A 584 " --> pdb=" O LYS A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 629 Processing helix chain 'A' and resid 645 through 651 Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'A' and resid 685 through 689 Processing helix chain 'A' and resid 698 through 703 removed outlier: 3.683A pdb=" N PHE A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 732 Processing helix chain 'A' and resid 752 through 756 removed outlier: 3.663A pdb=" N MET A 755 " --> pdb=" O ASP A 752 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 756 " --> pdb=" O PRO A 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 752 through 756' Processing helix chain 'A' and resid 759 through 765 removed outlier: 3.806A pdb=" N LEU A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 764 " --> pdb=" O MET A 760 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 765 " --> pdb=" O TYR A 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 759 through 765' Processing helix chain 'A' and resid 769 through 781 Processing helix chain 'A' and resid 785 through 810 removed outlier: 3.948A pdb=" N VAL A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY A 810 " --> pdb=" O GLU A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 846 Processing helix chain 'A' and resid 860 through 874 removed outlier: 4.143A pdb=" N VAL A 871 " --> pdb=" O ARG A 867 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N THR A 872 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 893 removed outlier: 3.619A pdb=" N GLY A 893 " --> pdb=" O LEU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 933 Processing helix chain 'A' and resid 949 through 963 Processing helix chain 'A' and resid 974 through 980 removed outlier: 3.646A pdb=" N ALA A 978 " --> pdb=" O GLY A 975 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN A 979 " --> pdb=" O ASP A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 988 Processing helix chain 'A' and resid 991 through 997 Processing helix chain 'A' and resid 1021 through 1029 removed outlier: 3.692A pdb=" N PHE A1025 " --> pdb=" O ARG A1021 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A1029 " --> pdb=" O PHE A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1055 Processing helix chain 'A' and resid 1068 through 1072 Processing helix chain 'A' and resid 1079 through 1084 Processing helix chain 'A' and resid 1099 through 1103 removed outlier: 3.657A pdb=" N LYS A1102 " --> pdb=" O ASP A1099 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A1103 " --> pdb=" O ALA A1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1099 through 1103' Processing helix chain 'A' and resid 1113 through 1125 removed outlier: 3.619A pdb=" N LYS A1119 " --> pdb=" O TYR A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1151 Processing helix chain 'A' and resid 1170 through 1182 removed outlier: 3.715A pdb=" N GLU A1176 " --> pdb=" O PRO A1172 " (cutoff:3.500A) Proline residue: A1179 - end of helix Processing helix chain 'A' and resid 1203 through 1219 Processing helix chain 'B' and resid 109 through 121 Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 135 through 152 Processing helix chain 'B' and resid 158 through 174 removed outlier: 3.596A pdb=" N ILE B 162 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 225 through 243 Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 288 through 292 removed outlier: 3.706A pdb=" N GLN B 292 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 320 through 335 Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.553A pdb=" N TRP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 384 through 387 removed outlier: 3.604A pdb=" N ALA B 387 " --> pdb=" O HIS B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 387' Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.840A pdb=" N LEU B 407 " --> pdb=" O HIS B 404 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP B 408 " --> pdb=" O ARG B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 427 through 431 Processing helix chain 'B' and resid 436 through 448 Processing helix chain 'B' and resid 460 through 474 removed outlier: 3.678A pdb=" N GLY B 474 " --> pdb=" O ARG B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 504 Processing helix chain 'B' and resid 517 through 533 Processing helix chain 'B' and resid 545 through 553 Processing helix chain 'B' and resid 557 through 566 removed outlier: 3.814A pdb=" N ILE B 561 " --> pdb=" O PRO B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 removed outlier: 3.924A pdb=" N LEU B 584 " --> pdb=" O LYS B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 629 Processing helix chain 'B' and resid 645 through 651 Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 685 through 689 Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.684A pdb=" N PHE B 702 " --> pdb=" O TYR B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 732 Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.663A pdb=" N MET B 755 " --> pdb=" O ASP B 752 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 756 " --> pdb=" O PRO B 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 752 through 756' Processing helix chain 'B' and resid 759 through 765 removed outlier: 3.807A pdb=" N LEU B 763 " --> pdb=" O LYS B 759 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 764 " --> pdb=" O MET B 760 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 765 " --> pdb=" O TYR B 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 759 through 765' Processing helix chain 'B' and resid 769 through 781 Processing helix chain 'B' and resid 785 through 810 removed outlier: 3.948A pdb=" N VAL B 793 " --> pdb=" O ALA B 789 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY B 810 " --> pdb=" O GLU B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 846 Processing helix chain 'B' and resid 860 through 874 removed outlier: 4.142A pdb=" N VAL B 871 " --> pdb=" O ARG B 867 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N THR B 872 " --> pdb=" O VAL B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 893 removed outlier: 3.619A pdb=" N GLY B 893 " --> pdb=" O LEU B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 933 Processing helix chain 'B' and resid 949 through 963 Processing helix chain 'B' and resid 974 through 980 removed outlier: 3.646A pdb=" N ALA B 978 " --> pdb=" O GLY B 975 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN B 979 " --> pdb=" O ASP B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 988 Processing helix chain 'B' and resid 991 through 997 Processing helix chain 'B' and resid 1021 through 1029 removed outlier: 3.692A pdb=" N PHE B1025 " --> pdb=" O ARG B1021 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS B1029 " --> pdb=" O PHE B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1055 Processing helix chain 'B' and resid 1068 through 1072 Processing helix chain 'B' and resid 1079 through 1084 Processing helix chain 'B' and resid 1099 through 1103 removed outlier: 3.657A pdb=" N LYS B1102 " --> pdb=" O ASP B1099 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B1103 " --> pdb=" O ALA B1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1099 through 1103' Processing helix chain 'B' and resid 1113 through 1125 removed outlier: 3.619A pdb=" N LYS B1119 " --> pdb=" O TYR B1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1151 Processing helix chain 'B' and resid 1170 through 1182 removed outlier: 3.714A pdb=" N GLU B1176 " --> pdb=" O PRO B1172 " (cutoff:3.500A) Proline residue: B1179 - end of helix Processing helix chain 'B' and resid 1203 through 1219 Processing helix chain 'C' and resid 109 through 121 Processing helix chain 'C' and resid 122 through 124 No H-bonds generated for 'chain 'C' and resid 122 through 124' Processing helix chain 'C' and resid 135 through 152 Processing helix chain 'C' and resid 158 through 174 removed outlier: 3.598A pdb=" N ILE C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 179 Processing helix chain 'C' and resid 225 through 243 Processing helix chain 'C' and resid 247 through 251 Processing helix chain 'C' and resid 288 through 292 removed outlier: 3.705A pdb=" N GLN C 292 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 320 through 335 Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.553A pdb=" N TRP C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 383 Processing helix chain 'C' and resid 384 through 387 removed outlier: 3.605A pdb=" N ALA C 387 " --> pdb=" O HIS C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 387' Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.839A pdb=" N LEU C 407 " --> pdb=" O HIS C 404 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 408 " --> pdb=" O ARG C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 436 through 448 Processing helix chain 'C' and resid 460 through 474 removed outlier: 3.679A pdb=" N GLY C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 504 Processing helix chain 'C' and resid 517 through 533 Processing helix chain 'C' and resid 545 through 553 Processing helix chain 'C' and resid 557 through 566 removed outlier: 3.814A pdb=" N ILE C 561 " --> pdb=" O PRO C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 584 removed outlier: 3.925A pdb=" N LEU C 584 " --> pdb=" O LYS C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 629 Processing helix chain 'C' and resid 645 through 651 Processing helix chain 'C' and resid 652 through 659 Processing helix chain 'C' and resid 685 through 689 Processing helix chain 'C' and resid 698 through 703 removed outlier: 3.684A pdb=" N PHE C 702 " --> pdb=" O TYR C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 732 Processing helix chain 'C' and resid 752 through 756 removed outlier: 3.664A pdb=" N MET C 755 " --> pdb=" O ASP C 752 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 756 " --> pdb=" O PRO C 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 752 through 756' Processing helix chain 'C' and resid 759 through 765 removed outlier: 3.806A pdb=" N LEU C 763 " --> pdb=" O LYS C 759 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 764 " --> pdb=" O MET C 760 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 765 " --> pdb=" O TYR C 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 759 through 765' Processing helix chain 'C' and resid 769 through 781 Processing helix chain 'C' and resid 785 through 810 removed outlier: 3.947A pdb=" N VAL C 793 " --> pdb=" O ALA C 789 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY C 810 " --> pdb=" O GLU C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 846 Processing helix chain 'C' and resid 860 through 874 removed outlier: 4.142A pdb=" N VAL C 871 " --> pdb=" O ARG C 867 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR C 872 " --> pdb=" O VAL C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 893 removed outlier: 3.619A pdb=" N GLY C 893 " --> pdb=" O LEU C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 933 Processing helix chain 'C' and resid 949 through 963 Processing helix chain 'C' and resid 974 through 980 removed outlier: 3.646A pdb=" N ALA C 978 " --> pdb=" O GLY C 975 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN C 979 " --> pdb=" O ASP C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 988 Processing helix chain 'C' and resid 991 through 997 Processing helix chain 'C' and resid 1021 through 1029 removed outlier: 3.692A pdb=" N PHE C1025 " --> pdb=" O ARG C1021 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS C1029 " --> pdb=" O PHE C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1055 Processing helix chain 'C' and resid 1068 through 1072 Processing helix chain 'C' and resid 1079 through 1084 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.657A pdb=" N LYS C1102 " --> pdb=" O ASP C1099 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C1103 " --> pdb=" O ALA C1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1099 through 1103' Processing helix chain 'C' and resid 1113 through 1125 removed outlier: 3.619A pdb=" N LYS C1119 " --> pdb=" O TYR C1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1151 Processing helix chain 'C' and resid 1170 through 1182 removed outlier: 3.714A pdb=" N GLU C1176 " --> pdb=" O PRO C1172 " (cutoff:3.500A) Proline residue: C1179 - end of helix Processing helix chain 'C' and resid 1203 through 1219 Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 122 through 124 No H-bonds generated for 'chain 'D' and resid 122 through 124' Processing helix chain 'D' and resid 135 through 152 Processing helix chain 'D' and resid 158 through 174 removed outlier: 3.594A pdb=" N ILE D 162 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 179 Processing helix chain 'D' and resid 225 through 243 Processing helix chain 'D' and resid 247 through 251 Processing helix chain 'D' and resid 288 through 292 removed outlier: 3.705A pdb=" N GLN D 292 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 303 Processing helix chain 'D' and resid 320 through 335 Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.554A pdb=" N TRP D 341 " --> pdb=" O ASP D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 383 Processing helix chain 'D' and resid 384 through 387 removed outlier: 3.605A pdb=" N ALA D 387 " --> pdb=" O HIS D 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 384 through 387' Processing helix chain 'D' and resid 404 through 408 removed outlier: 3.839A pdb=" N LEU D 407 " --> pdb=" O HIS D 404 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP D 408 " --> pdb=" O ARG D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 404 through 408' Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 427 through 431 Processing helix chain 'D' and resid 436 through 448 Processing helix chain 'D' and resid 460 through 474 removed outlier: 3.678A pdb=" N GLY D 474 " --> pdb=" O ARG D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 504 Processing helix chain 'D' and resid 517 through 533 Processing helix chain 'D' and resid 545 through 553 Processing helix chain 'D' and resid 557 through 566 removed outlier: 3.815A pdb=" N ILE D 561 " --> pdb=" O PRO D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 584 removed outlier: 3.924A pdb=" N LEU D 584 " --> pdb=" O LYS D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 629 Processing helix chain 'D' and resid 645 through 651 Processing helix chain 'D' and resid 652 through 659 Processing helix chain 'D' and resid 685 through 689 Processing helix chain 'D' and resid 698 through 703 removed outlier: 3.683A pdb=" N PHE D 702 " --> pdb=" O TYR D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 732 Processing helix chain 'D' and resid 752 through 756 removed outlier: 3.664A pdb=" N MET D 755 " --> pdb=" O ASP D 752 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR D 756 " --> pdb=" O PRO D 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 752 through 756' Processing helix chain 'D' and resid 759 through 765 removed outlier: 3.806A pdb=" N LEU D 763 " --> pdb=" O LYS D 759 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 764 " --> pdb=" O MET D 760 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR D 765 " --> pdb=" O TYR D 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 759 through 765' Processing helix chain 'D' and resid 769 through 781 Processing helix chain 'D' and resid 785 through 810 removed outlier: 3.948A pdb=" N VAL D 793 " --> pdb=" O ALA D 789 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY D 810 " --> pdb=" O GLU D 806 " (cutoff:3.500A) Processing helix chain 'D' and resid 836 through 846 Processing helix chain 'D' and resid 860 through 874 removed outlier: 4.144A pdb=" N VAL D 871 " --> pdb=" O ARG D 867 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N THR D 872 " --> pdb=" O VAL D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 877 through 893 removed outlier: 3.618A pdb=" N GLY D 893 " --> pdb=" O LEU D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 933 Processing helix chain 'D' and resid 949 through 963 Processing helix chain 'D' and resid 974 through 980 removed outlier: 3.646A pdb=" N ALA D 978 " --> pdb=" O GLY D 975 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN D 979 " --> pdb=" O ASP D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 981 through 988 Processing helix chain 'D' and resid 991 through 997 Processing helix chain 'D' and resid 1021 through 1029 removed outlier: 3.691A pdb=" N PHE D1025 " --> pdb=" O ARG D1021 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS D1029 " --> pdb=" O PHE D1025 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1055 Processing helix chain 'D' and resid 1068 through 1072 Processing helix chain 'D' and resid 1079 through 1084 Processing helix chain 'D' and resid 1099 through 1103 removed outlier: 3.657A pdb=" N LYS D1102 " --> pdb=" O ASP D1099 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D1103 " --> pdb=" O ALA D1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1099 through 1103' Processing helix chain 'D' and resid 1113 through 1125 removed outlier: 3.620A pdb=" N LYS D1119 " --> pdb=" O TYR D1115 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1151 Processing helix chain 'D' and resid 1170 through 1182 removed outlier: 3.714A pdb=" N GLU D1176 " --> pdb=" O PRO D1172 " (cutoff:3.500A) Proline residue: D1179 - end of helix Processing helix chain 'D' and resid 1203 through 1219 Processing helix chain 'E' and resid 109 through 121 Processing helix chain 'E' and resid 122 through 124 No H-bonds generated for 'chain 'E' and resid 122 through 124' Processing helix chain 'E' and resid 135 through 152 Processing helix chain 'E' and resid 158 through 174 removed outlier: 3.594A pdb=" N ILE E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 179 Processing helix chain 'E' and resid 225 through 243 Processing helix chain 'E' and resid 247 through 251 Processing helix chain 'E' and resid 288 through 292 removed outlier: 3.705A pdb=" N GLN E 292 " --> pdb=" O ALA E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 303 Processing helix chain 'E' and resid 320 through 335 Processing helix chain 'E' and resid 337 through 349 removed outlier: 3.552A pdb=" N TRP E 341 " --> pdb=" O ASP E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 383 Processing helix chain 'E' and resid 384 through 387 removed outlier: 3.606A pdb=" N ALA E 387 " --> pdb=" O HIS E 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 384 through 387' Processing helix chain 'E' and resid 404 through 408 removed outlier: 3.839A pdb=" N LEU E 407 " --> pdb=" O HIS E 404 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP E 408 " --> pdb=" O ARG E 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 404 through 408' Processing helix chain 'E' and resid 415 through 419 Processing helix chain 'E' and resid 427 through 431 Processing helix chain 'E' and resid 436 through 448 Processing helix chain 'E' and resid 460 through 474 removed outlier: 3.679A pdb=" N GLY E 474 " --> pdb=" O ARG E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 504 Processing helix chain 'E' and resid 517 through 533 Processing helix chain 'E' and resid 545 through 553 Processing helix chain 'E' and resid 557 through 566 removed outlier: 3.814A pdb=" N ILE E 561 " --> pdb=" O PRO E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 584 removed outlier: 3.924A pdb=" N LEU E 584 " --> pdb=" O LYS E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 613 through 629 Processing helix chain 'E' and resid 645 through 651 Processing helix chain 'E' and resid 652 through 659 Processing helix chain 'E' and resid 685 through 689 Processing helix chain 'E' and resid 698 through 703 removed outlier: 3.683A pdb=" N PHE E 702 " --> pdb=" O TYR E 698 " (cutoff:3.500A) Processing helix chain 'E' and resid 713 through 732 Processing helix chain 'E' and resid 752 through 756 removed outlier: 3.663A pdb=" N MET E 755 " --> pdb=" O ASP E 752 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR E 756 " --> pdb=" O PRO E 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 752 through 756' Processing helix chain 'E' and resid 759 through 765 removed outlier: 3.806A pdb=" N LEU E 763 " --> pdb=" O LYS E 759 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 764 " --> pdb=" O MET E 760 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR E 765 " --> pdb=" O TYR E 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 759 through 765' Processing helix chain 'E' and resid 769 through 781 Processing helix chain 'E' and resid 785 through 810 removed outlier: 3.948A pdb=" N VAL E 793 " --> pdb=" O ALA E 789 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE E 796 " --> pdb=" O VAL E 792 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY E 810 " --> pdb=" O GLU E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 836 through 846 Processing helix chain 'E' and resid 860 through 874 removed outlier: 4.143A pdb=" N VAL E 871 " --> pdb=" O ARG E 867 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N THR E 872 " --> pdb=" O VAL E 868 " (cutoff:3.500A) Processing helix chain 'E' and resid 877 through 893 removed outlier: 3.619A pdb=" N GLY E 893 " --> pdb=" O LEU E 889 " (cutoff:3.500A) Processing helix chain 'E' and resid 925 through 933 Processing helix chain 'E' and resid 949 through 963 Processing helix chain 'E' and resid 974 through 980 removed outlier: 3.646A pdb=" N ALA E 978 " --> pdb=" O GLY E 975 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN E 979 " --> pdb=" O ASP E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 981 through 988 Processing helix chain 'E' and resid 991 through 997 Processing helix chain 'E' and resid 1021 through 1029 removed outlier: 3.690A pdb=" N PHE E1025 " --> pdb=" O ARG E1021 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS E1029 " --> pdb=" O PHE E1025 " (cutoff:3.500A) Processing helix chain 'E' and resid 1041 through 1055 Processing helix chain 'E' and resid 1068 through 1072 Processing helix chain 'E' and resid 1079 through 1084 Processing helix chain 'E' and resid 1099 through 1103 removed outlier: 3.658A pdb=" N LYS E1102 " --> pdb=" O ASP E1099 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL E1103 " --> pdb=" O ALA E1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1099 through 1103' Processing helix chain 'E' and resid 1113 through 1125 removed outlier: 3.620A pdb=" N LYS E1119 " --> pdb=" O TYR E1115 " (cutoff:3.500A) Processing helix chain 'E' and resid 1141 through 1151 Processing helix chain 'E' and resid 1170 through 1182 removed outlier: 3.714A pdb=" N GLU E1176 " --> pdb=" O PRO E1172 " (cutoff:3.500A) Proline residue: E1179 - end of helix Processing helix chain 'E' and resid 1203 through 1219 Processing helix chain 'F' and resid 109 through 121 Processing helix chain 'F' and resid 122 through 124 No H-bonds generated for 'chain 'F' and resid 122 through 124' Processing helix chain 'F' and resid 135 through 152 Processing helix chain 'F' and resid 158 through 174 removed outlier: 3.596A pdb=" N ILE F 162 " --> pdb=" O SER F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 179 Processing helix chain 'F' and resid 225 through 243 Processing helix chain 'F' and resid 247 through 251 Processing helix chain 'F' and resid 288 through 292 removed outlier: 3.704A pdb=" N GLN F 292 " --> pdb=" O ALA F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 303 Processing helix chain 'F' and resid 320 through 335 Processing helix chain 'F' and resid 337 through 349 removed outlier: 3.549A pdb=" N TRP F 341 " --> pdb=" O ASP F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 383 Processing helix chain 'F' and resid 384 through 387 removed outlier: 3.605A pdb=" N ALA F 387 " --> pdb=" O HIS F 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 384 through 387' Processing helix chain 'F' and resid 404 through 408 removed outlier: 3.839A pdb=" N LEU F 407 " --> pdb=" O HIS F 404 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP F 408 " --> pdb=" O ARG F 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 404 through 408' Processing helix chain 'F' and resid 415 through 419 Processing helix chain 'F' and resid 427 through 431 Processing helix chain 'F' and resid 436 through 448 Processing helix chain 'F' and resid 460 through 474 removed outlier: 3.678A pdb=" N GLY F 474 " --> pdb=" O ARG F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 504 Processing helix chain 'F' and resid 517 through 533 Processing helix chain 'F' and resid 545 through 553 Processing helix chain 'F' and resid 557 through 566 removed outlier: 3.814A pdb=" N ILE F 561 " --> pdb=" O PRO F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 584 removed outlier: 3.925A pdb=" N LEU F 584 " --> pdb=" O LYS F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 629 Processing helix chain 'F' and resid 645 through 651 Processing helix chain 'F' and resid 652 through 659 Processing helix chain 'F' and resid 685 through 689 Processing helix chain 'F' and resid 698 through 703 removed outlier: 3.683A pdb=" N PHE F 702 " --> pdb=" O TYR F 698 " (cutoff:3.500A) Processing helix chain 'F' and resid 713 through 732 Processing helix chain 'F' and resid 752 through 756 removed outlier: 3.663A pdb=" N MET F 755 " --> pdb=" O ASP F 752 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR F 756 " --> pdb=" O PRO F 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 752 through 756' Processing helix chain 'F' and resid 759 through 765 removed outlier: 3.806A pdb=" N LEU F 763 " --> pdb=" O LYS F 759 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE F 764 " --> pdb=" O MET F 760 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR F 765 " --> pdb=" O TYR F 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 759 through 765' Processing helix chain 'F' and resid 769 through 781 Processing helix chain 'F' and resid 785 through 810 removed outlier: 3.947A pdb=" N VAL F 793 " --> pdb=" O ALA F 789 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE F 796 " --> pdb=" O VAL F 792 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY F 810 " --> pdb=" O GLU F 806 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 846 Processing helix chain 'F' and resid 860 through 874 removed outlier: 4.143A pdb=" N VAL F 871 " --> pdb=" O ARG F 867 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR F 872 " --> pdb=" O VAL F 868 " (cutoff:3.500A) Processing helix chain 'F' and resid 877 through 893 removed outlier: 3.619A pdb=" N GLY F 893 " --> pdb=" O LEU F 889 " (cutoff:3.500A) Processing helix chain 'F' and resid 925 through 933 Processing helix chain 'F' and resid 949 through 963 Processing helix chain 'F' and resid 974 through 980 removed outlier: 3.646A pdb=" N ALA F 978 " --> pdb=" O GLY F 975 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN F 979 " --> pdb=" O ASP F 976 " (cutoff:3.500A) Processing helix chain 'F' and resid 981 through 988 Processing helix chain 'F' and resid 991 through 997 Processing helix chain 'F' and resid 1021 through 1029 removed outlier: 3.691A pdb=" N PHE F1025 " --> pdb=" O ARG F1021 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS F1029 " --> pdb=" O PHE F1025 " (cutoff:3.500A) Processing helix chain 'F' and resid 1041 through 1055 Processing helix chain 'F' and resid 1068 through 1072 Processing helix chain 'F' and resid 1079 through 1084 Processing helix chain 'F' and resid 1099 through 1103 removed outlier: 3.657A pdb=" N LYS F1102 " --> pdb=" O ASP F1099 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL F1103 " --> pdb=" O ALA F1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1099 through 1103' Processing helix chain 'F' and resid 1113 through 1125 removed outlier: 3.619A pdb=" N LYS F1119 " --> pdb=" O TYR F1115 " (cutoff:3.500A) Processing helix chain 'F' and resid 1141 through 1151 Processing helix chain 'F' and resid 1170 through 1182 removed outlier: 3.714A pdb=" N GLU F1176 " --> pdb=" O PRO F1172 " (cutoff:3.500A) Proline residue: F1179 - end of helix Processing helix chain 'F' and resid 1203 through 1219 Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 218 removed outlier: 3.602A pdb=" N ALA A 201 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 256 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS C 267 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 184 Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 269 removed outlier: 3.591A pdb=" N HIS A 267 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER E 256 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA E 201 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 422 through 424 Processing sheet with id=AA6, first strand: chain 'A' and resid 451 through 454 removed outlier: 6.640A pdb=" N PHE A 707 " --> pdb=" O ASP A 738 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL A 740 " --> pdb=" O PHE A 707 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 709 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU A 536 " --> pdb=" O VAL A 638 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU A 640 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 538 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU A 642 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY A 540 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLY A 644 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL A 537 " --> pdb=" O SER A 602 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 939 through 944 removed outlier: 6.513A pdb=" N VAL A 896 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N TYR A 943 " --> pdb=" O VAL A 896 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 898 " --> pdb=" O TYR A 943 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU A1004 " --> pdb=" O ILE A1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR A1065 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A1006 " --> pdb=" O THR A1065 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR A1035 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE A1064 " --> pdb=" O THR A1035 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ALA A1037 " --> pdb=" O PHE A1064 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 915 through 916 Processing sheet with id=AA9, first strand: chain 'A' and resid 1091 through 1092 removed outlier: 6.781A pdb=" N LYS A1105 " --> pdb=" O ALA A1130 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL A1132 " --> pdb=" O LYS A1105 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N MET A1107 " --> pdb=" O VAL A1132 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE A1134 " --> pdb=" O MET A1107 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A1109 " --> pdb=" O ILE A1134 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG A1193 " --> pdb=" O GLN A1162 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU A1164 " --> pdb=" O ARG A1193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB2, first strand: chain 'B' and resid 211 through 218 removed outlier: 3.599A pdb=" N ALA B 201 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 256 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS F 267 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 180 through 184 Processing sheet with id=AB4, first strand: chain 'B' and resid 267 through 269 removed outlier: 3.590A pdb=" N HIS B 267 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER D 256 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 201 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 422 through 424 Processing sheet with id=AB6, first strand: chain 'B' and resid 451 through 454 removed outlier: 6.640A pdb=" N PHE B 707 " --> pdb=" O ASP B 738 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL B 740 " --> pdb=" O PHE B 707 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B 709 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU B 536 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU B 640 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL B 538 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU B 642 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY B 540 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY B 644 " --> pdb=" O GLY B 540 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL B 537 " --> pdb=" O SER B 602 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 939 through 944 removed outlier: 6.512A pdb=" N VAL B 896 " --> pdb=" O LEU B 941 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N TYR B 943 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU B 898 " --> pdb=" O TYR B 943 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B1004 " --> pdb=" O ILE B1063 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR B1065 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU B1006 " --> pdb=" O THR B1065 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR B1035 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N PHE B1064 " --> pdb=" O THR B1035 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ALA B1037 " --> pdb=" O PHE B1064 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 915 through 916 Processing sheet with id=AB9, first strand: chain 'B' and resid 1091 through 1092 removed outlier: 6.782A pdb=" N LYS B1105 " --> pdb=" O ALA B1130 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL B1132 " --> pdb=" O LYS B1105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET B1107 " --> pdb=" O VAL B1132 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE B1134 " --> pdb=" O MET B1107 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B1109 " --> pdb=" O ILE B1134 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG B1193 " --> pdb=" O GLN B1162 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU B1164 " --> pdb=" O ARG B1193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 211 through 218 removed outlier: 3.600A pdb=" N ALA C 201 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER C 256 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS E 267 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 180 through 184 Processing sheet with id=AC3, first strand: chain 'C' and resid 422 through 424 Processing sheet with id=AC4, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.640A pdb=" N PHE C 707 " --> pdb=" O ASP C 738 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL C 740 " --> pdb=" O PHE C 707 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL C 709 " --> pdb=" O VAL C 740 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU C 536 " --> pdb=" O VAL C 638 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU C 640 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 538 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU C 642 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY C 540 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY C 644 " --> pdb=" O GLY C 540 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL C 537 " --> pdb=" O SER C 602 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 939 through 944 removed outlier: 6.512A pdb=" N VAL C 896 " --> pdb=" O LEU C 941 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N TYR C 943 " --> pdb=" O VAL C 896 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU C 898 " --> pdb=" O TYR C 943 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU C1004 " --> pdb=" O ILE C1063 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR C1065 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU C1006 " --> pdb=" O THR C1065 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR C1035 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N PHE C1064 " --> pdb=" O THR C1035 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ALA C1037 " --> pdb=" O PHE C1064 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 915 through 916 Processing sheet with id=AC7, first strand: chain 'C' and resid 1091 through 1092 removed outlier: 6.781A pdb=" N LYS C1105 " --> pdb=" O ALA C1130 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL C1132 " --> pdb=" O LYS C1105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET C1107 " --> pdb=" O VAL C1132 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE C1134 " --> pdb=" O MET C1107 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C1109 " --> pdb=" O ILE C1134 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG C1193 " --> pdb=" O GLN C1162 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU C1164 " --> pdb=" O ARG C1193 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 103 through 106 Processing sheet with id=AC9, first strand: chain 'D' and resid 267 through 269 removed outlier: 3.592A pdb=" N HIS D 267 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER F 256 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA F 201 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 422 through 424 Processing sheet with id=AD2, first strand: chain 'D' and resid 451 through 454 removed outlier: 6.639A pdb=" N PHE D 707 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL D 740 " --> pdb=" O PHE D 707 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL D 709 " --> pdb=" O VAL D 740 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU D 536 " --> pdb=" O VAL D 638 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU D 640 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL D 538 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU D 642 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY D 540 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N GLY D 644 " --> pdb=" O GLY D 540 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL D 537 " --> pdb=" O SER D 602 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 939 through 944 removed outlier: 6.513A pdb=" N VAL D 896 " --> pdb=" O LEU D 941 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N TYR D 943 " --> pdb=" O VAL D 896 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU D 898 " --> pdb=" O TYR D 943 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU D1004 " --> pdb=" O ILE D1063 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR D1065 " --> pdb=" O LEU D1004 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU D1006 " --> pdb=" O THR D1065 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR D1035 " --> pdb=" O VAL D1062 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE D1064 " --> pdb=" O THR D1035 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ALA D1037 " --> pdb=" O PHE D1064 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 915 through 916 Processing sheet with id=AD5, first strand: chain 'D' and resid 1091 through 1092 removed outlier: 6.781A pdb=" N LYS D1105 " --> pdb=" O ALA D1130 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL D1132 " --> pdb=" O LYS D1105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET D1107 " --> pdb=" O VAL D1132 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE D1134 " --> pdb=" O MET D1107 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL D1109 " --> pdb=" O ILE D1134 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG D1193 " --> pdb=" O GLN D1162 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU D1164 " --> pdb=" O ARG D1193 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 422 through 424 Processing sheet with id=AD7, first strand: chain 'E' and resid 451 through 454 removed outlier: 6.639A pdb=" N PHE E 707 " --> pdb=" O ASP E 738 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL E 740 " --> pdb=" O PHE E 707 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL E 709 " --> pdb=" O VAL E 740 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU E 536 " --> pdb=" O VAL E 638 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU E 640 " --> pdb=" O GLU E 536 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL E 538 " --> pdb=" O LEU E 640 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU E 642 " --> pdb=" O VAL E 538 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY E 540 " --> pdb=" O LEU E 642 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY E 644 " --> pdb=" O GLY E 540 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL E 537 " --> pdb=" O SER E 602 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 939 through 944 removed outlier: 6.513A pdb=" N VAL E 896 " --> pdb=" O LEU E 941 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N TYR E 943 " --> pdb=" O VAL E 896 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU E 898 " --> pdb=" O TYR E 943 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU E1004 " --> pdb=" O ILE E1063 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR E1065 " --> pdb=" O LEU E1004 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU E1006 " --> pdb=" O THR E1065 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR E1035 " --> pdb=" O VAL E1062 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE E1064 " --> pdb=" O THR E1035 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ALA E1037 " --> pdb=" O PHE E1064 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 915 through 916 Processing sheet with id=AE1, first strand: chain 'E' and resid 1091 through 1092 removed outlier: 6.781A pdb=" N LYS E1105 " --> pdb=" O ALA E1130 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL E1132 " --> pdb=" O LYS E1105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET E1107 " --> pdb=" O VAL E1132 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE E1134 " --> pdb=" O MET E1107 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL E1109 " --> pdb=" O ILE E1134 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG E1193 " --> pdb=" O GLN E1162 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU E1164 " --> pdb=" O ARG E1193 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 422 through 424 Processing sheet with id=AE3, first strand: chain 'F' and resid 451 through 454 removed outlier: 6.639A pdb=" N PHE F 707 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL F 740 " --> pdb=" O PHE F 707 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL F 709 " --> pdb=" O VAL F 740 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU F 536 " --> pdb=" O VAL F 638 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU F 640 " --> pdb=" O GLU F 536 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL F 538 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU F 642 " --> pdb=" O VAL F 538 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY F 540 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N GLY F 644 " --> pdb=" O GLY F 540 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL F 537 " --> pdb=" O SER F 602 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 939 through 944 removed outlier: 6.513A pdb=" N VAL F 896 " --> pdb=" O LEU F 941 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N TYR F 943 " --> pdb=" O VAL F 896 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU F 898 " --> pdb=" O TYR F 943 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU F1004 " --> pdb=" O ILE F1063 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR F1065 " --> pdb=" O LEU F1004 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU F1006 " --> pdb=" O THR F1065 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR F1035 " --> pdb=" O VAL F1062 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE F1064 " --> pdb=" O THR F1035 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ALA F1037 " --> pdb=" O PHE F1064 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 915 through 916 Processing sheet with id=AE6, first strand: chain 'F' and resid 1091 through 1092 removed outlier: 6.782A pdb=" N LYS F1105 " --> pdb=" O ALA F1130 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL F1132 " --> pdb=" O LYS F1105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET F1107 " --> pdb=" O VAL F1132 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE F1134 " --> pdb=" O MET F1107 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL F1109 " --> pdb=" O ILE F1134 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG F1193 " --> pdb=" O GLN F1162 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU F1164 " --> pdb=" O ARG F1193 " (cutoff:3.500A) 2490 hydrogen bonds defined for protein. 7002 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: 25.95 Time building geometry restraints manager: 14.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 11718 1.33 - 1.45: 16360 1.45 - 1.58: 25136 1.58 - 1.71: 60 1.71 - 1.83: 426 Bond restraints: 53700 Sorted by residual: bond pdb=" C5 TPP E1303 " pdb=" S1 TPP E1303 " ideal model delta sigma weight residual 1.727 1.624 0.103 1.00e-02 1.00e+04 1.06e+02 bond pdb=" C5 TPP C1303 " pdb=" S1 TPP C1303 " ideal model delta sigma weight residual 1.727 1.624 0.103 1.00e-02 1.00e+04 1.05e+02 bond pdb=" C5 TPP F1303 " pdb=" S1 TPP F1303 " ideal model delta sigma weight residual 1.727 1.625 0.102 1.00e-02 1.00e+04 1.05e+02 bond pdb=" C5 TPP D1303 " pdb=" S1 TPP D1303 " ideal model delta sigma weight residual 1.727 1.625 0.102 1.00e-02 1.00e+04 1.04e+02 bond pdb=" C5 TPP A1303 " pdb=" S1 TPP A1303 " ideal model delta sigma weight residual 1.727 1.626 0.101 1.00e-02 1.00e+04 1.03e+02 ... (remaining 53695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 71169 3.01 - 6.03: 1561 6.03 - 9.04: 75 9.04 - 12.06: 5 12.06 - 15.07: 6 Bond angle restraints: 72816 Sorted by residual: angle pdb=" C ACO C1302 " pdb=" S1P ACO C1302 " pdb=" C2P ACO C1302 " ideal model delta sigma weight residual 101.25 109.38 -8.13 1.00e+00 1.00e+00 6.60e+01 angle pdb=" C ACO E1302 " pdb=" S1P ACO E1302 " pdb=" C2P ACO E1302 " ideal model delta sigma weight residual 101.25 109.31 -8.06 1.00e+00 1.00e+00 6.50e+01 angle pdb=" C ACO B1302 " pdb=" S1P ACO B1302 " pdb=" C2P ACO B1302 " ideal model delta sigma weight residual 101.25 109.11 -7.86 1.00e+00 1.00e+00 6.18e+01 angle pdb=" C ACO F1302 " pdb=" S1P ACO F1302 " pdb=" C2P ACO F1302 " ideal model delta sigma weight residual 101.25 108.93 -7.68 1.00e+00 1.00e+00 5.89e+01 angle pdb=" C ACO D1302 " pdb=" S1P ACO D1302 " pdb=" C2P ACO D1302 " ideal model delta sigma weight residual 101.25 108.49 -7.24 1.00e+00 1.00e+00 5.24e+01 ... (remaining 72811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 29772 17.82 - 35.64: 1906 35.64 - 53.45: 437 53.45 - 71.27: 218 71.27 - 89.09: 31 Dihedral angle restraints: 32364 sinusoidal: 13212 harmonic: 19152 Sorted by residual: dihedral pdb=" CA LEU A 307 " pdb=" C LEU A 307 " pdb=" N VAL A 308 " pdb=" CA VAL A 308 " ideal model delta harmonic sigma weight residual 180.00 153.63 26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA LEU B 307 " pdb=" C LEU B 307 " pdb=" N VAL B 308 " pdb=" CA VAL B 308 " ideal model delta harmonic sigma weight residual 180.00 153.63 26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA LEU D 307 " pdb=" C LEU D 307 " pdb=" N VAL D 308 " pdb=" CA VAL D 308 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 32361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 5341 0.079 - 0.159: 2328 0.159 - 0.238: 234 0.238 - 0.317: 12 0.317 - 0.397: 17 Chirality restraints: 7932 Sorted by residual: chirality pdb=" CA PRO C 714 " pdb=" N PRO C 714 " pdb=" C PRO C 714 " pdb=" CB PRO C 714 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA PRO D 714 " pdb=" N PRO D 714 " pdb=" C PRO D 714 " pdb=" CB PRO D 714 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA PRO A 714 " pdb=" N PRO A 714 " pdb=" C PRO A 714 " pdb=" CB PRO A 714 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.74e+00 ... (remaining 7929 not shown) Planarity restraints: 9594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P ACO A1302 " -0.071 2.00e-02 2.50e+03 5.86e-02 4.30e+01 pdb=" C5P ACO A1302 " 0.015 2.00e-02 2.50e+03 pdb=" C6P ACO A1302 " -0.052 2.00e-02 2.50e+03 pdb=" N4P ACO A1302 " 0.095 2.00e-02 2.50e+03 pdb=" O5P ACO A1302 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO E1302 " -0.068 2.00e-02 2.50e+03 5.62e-02 3.94e+01 pdb=" C5P ACO E1302 " 0.015 2.00e-02 2.50e+03 pdb=" C6P ACO E1302 " -0.050 2.00e-02 2.50e+03 pdb=" N4P ACO E1302 " 0.091 2.00e-02 2.50e+03 pdb=" O5P ACO E1302 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO F1302 " 0.062 2.00e-02 2.50e+03 5.14e-02 3.30e+01 pdb=" C5P ACO F1302 " -0.014 2.00e-02 2.50e+03 pdb=" C6P ACO F1302 " 0.046 2.00e-02 2.50e+03 pdb=" N4P ACO F1302 " -0.083 2.00e-02 2.50e+03 pdb=" O5P ACO F1302 " -0.011 2.00e-02 2.50e+03 ... (remaining 9591 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 876 2.68 - 3.23: 46304 3.23 - 3.79: 73397 3.79 - 4.34: 109353 4.34 - 4.90: 179057 Nonbonded interactions: 408987 Sorted by model distance: nonbonded pdb="MG MG A1301 " pdb=" O2B TPP A1303 " model vdw 2.125 2.170 nonbonded pdb="MG MG E1301 " pdb=" O2B TPP E1303 " model vdw 2.127 2.170 nonbonded pdb="MG MG F1301 " pdb=" O2B TPP F1303 " model vdw 2.136 2.170 nonbonded pdb="MG MG C1301 " pdb=" O2B TPP C1303 " model vdw 2.137 2.170 nonbonded pdb="MG MG B1301 " pdb=" O2B TPP B1303 " model vdw 2.140 2.170 ... (remaining 408982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 2.050 Check model and map are aligned: 0.430 Set scattering table: 0.440 Process input model: 109.990 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.280 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:13.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 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 : 0.011 0.103 53700 Z= 0.694 Angle : 1.215 15.071 72816 Z= 0.824 Chirality : 0.078 0.397 7932 Planarity : 0.008 0.104 9594 Dihedral : 13.970 89.090 20112 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.42 % Allowed : 2.58 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.08), residues: 6702 helix: -1.46 (0.08), residues: 2694 sheet: 0.12 (0.14), residues: 1098 loop : -1.88 (0.09), residues: 2910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.006 TRP C 466 HIS 0.015 0.004 HIS B 857 PHE 0.032 0.004 PHE E1046 TYR 0.056 0.006 TYR A 761 ARG 0.010 0.002 ARG E1144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1289 time to evaluate : 5.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8833 (mmp) cc_final: 0.8535 (mmt) REVERT: A 290 GLU cc_start: 0.8715 (pm20) cc_final: 0.8441 (pm20) REVERT: A 296 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8581 (mm-30) REVERT: A 377 GLU cc_start: 0.8368 (tt0) cc_final: 0.8128 (tt0) REVERT: A 434 MET cc_start: 0.9067 (ttm) cc_final: 0.8737 (mtp) REVERT: A 760 MET cc_start: 0.9154 (ttt) cc_final: 0.8851 (ttp) REVERT: A 808 LYS cc_start: 0.8495 (mttt) cc_final: 0.8279 (mttt) REVERT: B 118 MET cc_start: 0.8859 (mmp) cc_final: 0.8551 (mmt) REVERT: B 290 GLU cc_start: 0.8728 (pm20) cc_final: 0.8471 (pm20) REVERT: B 296 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8576 (mm-30) REVERT: B 377 GLU cc_start: 0.8372 (tt0) cc_final: 0.8129 (tt0) REVERT: B 760 MET cc_start: 0.9157 (ttt) cc_final: 0.8861 (ttp) REVERT: B 808 LYS cc_start: 0.8493 (mttt) cc_final: 0.8278 (mttt) REVERT: C 404 HIS cc_start: 0.8845 (p90) cc_final: 0.8624 (p-80) REVERT: C 434 MET cc_start: 0.9060 (ttm) cc_final: 0.8777 (mtt) REVERT: D 118 MET cc_start: 0.8800 (mmp) cc_final: 0.8227 (mmt) REVERT: D 296 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8555 (mm-30) REVERT: D 800 MET cc_start: 0.8824 (mtm) cc_final: 0.8619 (mtp) REVERT: D 1122 GLU cc_start: 0.8775 (tp30) cc_final: 0.8535 (tp30) REVERT: D 1185 MET cc_start: 0.9149 (ttp) cc_final: 0.8801 (ttp) REVERT: E 113 SER cc_start: 0.8906 (m) cc_final: 0.8666 (p) REVERT: E 185 ASP cc_start: 0.8413 (t70) cc_final: 0.8187 (t0) REVERT: E 800 MET cc_start: 0.8825 (mtm) cc_final: 0.8614 (mtp) REVERT: E 1122 GLU cc_start: 0.8774 (tp30) cc_final: 0.8545 (tp30) REVERT: E 1185 MET cc_start: 0.9144 (ttp) cc_final: 0.8792 (ttp) REVERT: F 190 LEU cc_start: 0.9129 (tp) cc_final: 0.8922 (tp) REVERT: F 296 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8556 (mm-30) REVERT: F 404 HIS cc_start: 0.8856 (p90) cc_final: 0.8643 (p-80) REVERT: F 1027 GLN cc_start: 0.8734 (mt0) cc_final: 0.8445 (mt0) outliers start: 23 outliers final: 7 residues processed: 1300 average time/residue: 2.0214 time to fit residues: 3180.1616 Evaluate side-chains 1215 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1208 time to evaluate : 5.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 397 PRO Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain E residue 682 PHE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 397 PRO Chi-restraints excluded: chain F residue 682 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 562 optimal weight: 3.9990 chunk 504 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 340 optimal weight: 3.9990 chunk 269 optimal weight: 0.8980 chunk 522 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 317 optimal weight: 0.7980 chunk 388 optimal weight: 0.9980 chunk 604 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 404 HIS A 501 GLN A 849 ASN B 195 HIS B 501 GLN B1072 ASN B1096 ASN C 292 GLN C 359 GLN C 498 ASN C 501 GLN C 799 GLN C 849 ASN C1072 ASN D 320 GLN D 404 HIS D 501 GLN D 799 GLN D 849 ASN D1072 ASN E 292 GLN E 320 GLN E 404 HIS E 501 GLN E 589 GLN E 799 GLN F 292 GLN F 501 GLN F 849 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1072 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 53700 Z= 0.183 Angle : 0.557 7.482 72816 Z= 0.296 Chirality : 0.043 0.140 7932 Planarity : 0.005 0.045 9594 Dihedral : 7.326 74.569 7672 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.83 % Allowed : 8.80 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.09), residues: 6702 helix: 0.90 (0.09), residues: 2742 sheet: 0.82 (0.15), residues: 1074 loop : -1.45 (0.10), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 466 HIS 0.005 0.001 HIS B 643 PHE 0.027 0.001 PHE B1046 TYR 0.013 0.001 TYR C 761 ARG 0.007 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 1182 time to evaluate : 5.647 Fit side-chains REVERT: A 290 GLU cc_start: 0.8578 (pm20) cc_final: 0.8288 (pm20) REVERT: A 377 GLU cc_start: 0.8300 (tt0) cc_final: 0.8061 (tt0) REVERT: A 434 MET cc_start: 0.8928 (ttm) cc_final: 0.8642 (mtp) REVERT: A 543 HIS cc_start: 0.8777 (p-80) cc_final: 0.8567 (p90) REVERT: A 760 MET cc_start: 0.9103 (ttt) cc_final: 0.8800 (ttt) REVERT: B 290 GLU cc_start: 0.8582 (pm20) cc_final: 0.8311 (pm20) REVERT: B 377 GLU cc_start: 0.8294 (tt0) cc_final: 0.8057 (tt0) REVERT: B 405 ARG cc_start: 0.8798 (mtm180) cc_final: 0.8562 (mtp180) REVERT: B 434 MET cc_start: 0.8922 (ttm) cc_final: 0.8658 (mtp) REVERT: B 543 HIS cc_start: 0.8771 (p-80) cc_final: 0.8558 (p90) REVERT: B 760 MET cc_start: 0.9108 (ttt) cc_final: 0.8828 (ttt) REVERT: B 801 GLU cc_start: 0.8917 (tp30) cc_final: 0.8709 (mm-30) REVERT: B 1027 GLN cc_start: 0.8507 (mt0) cc_final: 0.8242 (mt0) REVERT: C 113 SER cc_start: 0.8704 (m) cc_final: 0.8436 (p) REVERT: C 404 HIS cc_start: 0.8661 (p90) cc_final: 0.8445 (p-80) REVERT: C 801 GLU cc_start: 0.8948 (tp30) cc_final: 0.8674 (mm-30) REVERT: C 1027 GLN cc_start: 0.8554 (mt0) cc_final: 0.8328 (mt0) REVERT: D 118 MET cc_start: 0.8798 (mmp) cc_final: 0.8207 (mmt) REVERT: D 271 ARG cc_start: 0.8940 (mmm160) cc_final: 0.8575 (mtp180) REVERT: D 296 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8483 (mm-30) REVERT: E 113 SER cc_start: 0.8774 (m) cc_final: 0.8549 (p) REVERT: E 185 ASP cc_start: 0.8094 (t70) cc_final: 0.7836 (t0) REVERT: F 190 LEU cc_start: 0.9018 (tp) cc_final: 0.8792 (tp) REVERT: F 404 HIS cc_start: 0.8668 (p90) cc_final: 0.8458 (p-80) REVERT: F 541 MET cc_start: 0.8995 (ptm) cc_final: 0.8775 (ptm) outliers start: 46 outliers final: 15 residues processed: 1193 average time/residue: 2.0910 time to fit residues: 3009.9300 Evaluate side-chains 1159 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 1144 time to evaluate : 5.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 1175 GLN Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 1175 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 336 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 503 optimal weight: 3.9990 chunk 411 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 605 optimal weight: 5.9990 chunk 654 optimal weight: 0.9980 chunk 539 optimal weight: 0.9990 chunk 600 optimal weight: 0.0170 chunk 206 optimal weight: 0.5980 chunk 486 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 404 HIS A 799 GLN A 818 GLN A1096 ASN B 424 ASN B 786 ASN B 799 GLN ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 ASN B1096 ASN B1213 GLN C 148 GLN C 251 GLN C 590 HIS C 944 ASN C1096 ASN D 225 ASN D 404 HIS D 501 GLN D 773 GLN D 799 GLN E 292 GLN E 404 HIS E 501 GLN E 773 GLN E 799 GLN F 225 ASN F 849 ASN F 944 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1096 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 53700 Z= 0.151 Angle : 0.495 8.568 72816 Z= 0.258 Chirality : 0.042 0.135 7932 Planarity : 0.004 0.043 9594 Dihedral : 6.845 65.781 7656 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.96 % Allowed : 10.68 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.10), residues: 6702 helix: 1.87 (0.10), residues: 2772 sheet: 0.88 (0.15), residues: 1104 loop : -1.19 (0.10), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 466 HIS 0.004 0.001 HIS E 643 PHE 0.024 0.001 PHE A1046 TYR 0.012 0.001 TYR A 233 ARG 0.007 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1243 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 1190 time to evaluate : 5.867 Fit side-chains REVERT: A 113 SER cc_start: 0.8618 (t) cc_final: 0.8382 (p) REVERT: A 290 GLU cc_start: 0.8556 (pm20) cc_final: 0.8258 (pm20) REVERT: A 377 GLU cc_start: 0.8270 (tt0) cc_final: 0.8021 (tt0) REVERT: A 434 MET cc_start: 0.8874 (ttm) cc_final: 0.8637 (mtp) REVERT: A 543 HIS cc_start: 0.8713 (p-80) cc_final: 0.8505 (p90) REVERT: A 760 MET cc_start: 0.9054 (ttt) cc_final: 0.8798 (ttt) REVERT: B 113 SER cc_start: 0.8605 (t) cc_final: 0.8371 (p) REVERT: B 290 GLU cc_start: 0.8560 (pm20) cc_final: 0.8250 (pm20) REVERT: B 377 GLU cc_start: 0.8274 (tt0) cc_final: 0.8047 (tt0) REVERT: B 760 MET cc_start: 0.9065 (ttt) cc_final: 0.8818 (ttt) REVERT: C 113 SER cc_start: 0.8687 (m) cc_final: 0.8451 (p) REVERT: C 801 GLU cc_start: 0.8954 (tp30) cc_final: 0.8697 (mm-30) REVERT: D 118 MET cc_start: 0.8787 (mmp) cc_final: 0.8141 (mmt) REVERT: D 271 ARG cc_start: 0.8906 (mmm160) cc_final: 0.8642 (mtp180) REVERT: D 800 MET cc_start: 0.8571 (mtm) cc_final: 0.8359 (mtp) REVERT: F 190 LEU cc_start: 0.9020 (tp) cc_final: 0.8772 (tp) REVERT: F 296 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8440 (mm-30) outliers start: 53 outliers final: 25 residues processed: 1194 average time/residue: 2.0220 time to fit residues: 2923.8263 Evaluate side-chains 1185 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 1160 time to evaluate : 5.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 1175 GLN Chi-restraints excluded: chain C residue 1209 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 1209 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 598 optimal weight: 0.6980 chunk 455 optimal weight: 4.9990 chunk 314 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 406 optimal weight: 0.8980 chunk 608 optimal weight: 0.4980 chunk 643 optimal weight: 0.8980 chunk 317 optimal weight: 3.9990 chunk 576 optimal weight: 0.0980 chunk 173 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 404 HIS A 590 HIS A 799 GLN A1213 GLN B 404 HIS B 799 GLN B 818 GLN ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN C 251 GLN C 359 GLN C 404 HIS C 424 ASN C 773 GLN C1096 ASN D 195 HIS D 349 ASN D 404 HIS D 799 GLN E 292 GLN E 349 ASN E 404 HIS E 488 GLN E 799 GLN F 148 GLN F 404 HIS F 773 GLN F 944 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1096 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 53700 Z= 0.143 Angle : 0.476 8.602 72816 Z= 0.247 Chirality : 0.042 0.135 7932 Planarity : 0.004 0.045 9594 Dihedral : 6.632 64.768 7656 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.07 % Allowed : 11.61 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.10), residues: 6702 helix: 2.26 (0.10), residues: 2784 sheet: 1.03 (0.15), residues: 1080 loop : -1.04 (0.10), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 466 HIS 0.004 0.001 HIS F1045 PHE 0.024 0.001 PHE C1046 TYR 0.013 0.001 TYR C 582 ARG 0.011 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 1206 time to evaluate : 5.600 Fit side-chains revert: symmetry clash REVERT: A 290 GLU cc_start: 0.8556 (pm20) cc_final: 0.8295 (pm20) REVERT: A 377 GLU cc_start: 0.8267 (tt0) cc_final: 0.8014 (tt0) REVERT: A 434 MET cc_start: 0.8836 (ttm) cc_final: 0.8617 (mtp) REVERT: B 113 SER cc_start: 0.8594 (t) cc_final: 0.8367 (p) REVERT: B 118 MET cc_start: 0.8958 (mmt) cc_final: 0.8614 (mmt) REVERT: B 290 GLU cc_start: 0.8557 (pm20) cc_final: 0.8285 (pm20) REVERT: B 377 GLU cc_start: 0.8267 (tt0) cc_final: 0.8011 (tt0) REVERT: B 448 THR cc_start: 0.8601 (m) cc_final: 0.8202 (m) REVERT: B 760 MET cc_start: 0.9022 (ttt) cc_final: 0.8808 (ttt) REVERT: C 113 SER cc_start: 0.8680 (m) cc_final: 0.8446 (p) REVERT: C 801 GLU cc_start: 0.8929 (tp30) cc_final: 0.8666 (mm-30) REVERT: D 118 MET cc_start: 0.8786 (mmp) cc_final: 0.8252 (mmt) REVERT: D 271 ARG cc_start: 0.8855 (mmm160) cc_final: 0.8638 (mtp180) REVERT: D 800 MET cc_start: 0.8533 (mtm) cc_final: 0.8304 (mtt) REVERT: D 1056 ASP cc_start: 0.8407 (t70) cc_final: 0.8200 (t0) REVERT: E 501 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8113 (tp40) REVERT: E 1027 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8329 (mt0) REVERT: F 190 LEU cc_start: 0.9019 (tp) cc_final: 0.8773 (tp) REVERT: F 296 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8435 (mm-30) REVERT: F 395 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8934 (p) outliers start: 59 outliers final: 25 residues processed: 1217 average time/residue: 2.0378 time to fit residues: 2998.6973 Evaluate side-chains 1216 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 1188 time to evaluate : 5.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 826 LYS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 1175 GLN Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 501 GLN Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 920 THR Chi-restraints excluded: chain E residue 1027 GLN Chi-restraints excluded: chain E residue 1175 GLN Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 247 MET Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 726 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 536 optimal weight: 4.9990 chunk 365 optimal weight: 4.9990 chunk 9 optimal weight: 0.0570 chunk 479 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 549 optimal weight: 0.5980 chunk 444 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 328 optimal weight: 2.9990 chunk 577 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 404 HIS A 799 GLN A1096 ASN B 404 HIS B 590 HIS B 799 GLN B1096 ASN C 148 GLN C 404 HIS C 424 ASN C 799 GLN C 944 ASN C1096 ASN D 195 HIS D 349 ASN D 404 HIS D 488 GLN D 799 GLN D1027 GLN E 404 HIS E 799 GLN F 148 GLN F 404 HIS F 944 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1096 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 53700 Z= 0.331 Angle : 0.573 9.730 72816 Z= 0.302 Chirality : 0.047 0.157 7932 Planarity : 0.005 0.047 9594 Dihedral : 6.932 67.957 7656 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.16 % Allowed : 12.22 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.10), residues: 6702 helix: 2.13 (0.10), residues: 2784 sheet: 0.91 (0.15), residues: 1062 loop : -1.12 (0.10), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 466 HIS 0.008 0.001 HIS F 267 PHE 0.031 0.002 PHE C1046 TYR 0.020 0.002 TYR C 761 ARG 0.009 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1210 time to evaluate : 5.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 GLU cc_start: 0.8685 (pm20) cc_final: 0.8398 (pm20) REVERT: A 377 GLU cc_start: 0.8313 (tt0) cc_final: 0.8077 (tt0) REVERT: A 434 MET cc_start: 0.8894 (ttm) cc_final: 0.8622 (ttm) REVERT: A 1027 GLN cc_start: 0.8554 (mt0) cc_final: 0.8255 (mt0) REVERT: B 118 MET cc_start: 0.8940 (mmt) cc_final: 0.8575 (mmt) REVERT: B 290 GLU cc_start: 0.8683 (pm20) cc_final: 0.8371 (pm20) REVERT: B 377 GLU cc_start: 0.8318 (tt0) cc_final: 0.8080 (tt0) REVERT: B 1208 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8476 (mt0) REVERT: C 801 GLU cc_start: 0.8958 (tp30) cc_final: 0.8703 (mm-30) REVERT: D 118 MET cc_start: 0.8777 (mmp) cc_final: 0.8220 (mmt) REVERT: E 501 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8364 (tp40) REVERT: F 190 LEU cc_start: 0.9057 (tp) cc_final: 0.8839 (tp) outliers start: 64 outliers final: 32 residues processed: 1218 average time/residue: 2.0567 time to fit residues: 3029.1318 Evaluate side-chains 1226 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 1192 time to evaluate : 6.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1208 GLN Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 501 GLN Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 247 MET Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 433 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 216 optimal weight: 0.5980 chunk 579 optimal weight: 0.9990 chunk 127 optimal weight: 0.0050 chunk 377 optimal weight: 0.7980 chunk 158 optimal weight: 7.9990 chunk 644 optimal weight: 3.9990 chunk 534 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 213 optimal weight: 0.9990 chunk 338 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 404 HIS A 786 ASN A 799 GLN B 404 HIS B 424 ASN B 799 GLN C 148 GLN C 404 HIS C 424 ASN C 944 ASN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1096 ASN D 195 HIS D 404 HIS D 799 GLN D1072 ASN E 292 GLN E 404 HIS E 799 GLN F 148 GLN F 225 ASN F 404 HIS F 944 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1096 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 53700 Z= 0.153 Angle : 0.483 9.070 72816 Z= 0.251 Chirality : 0.042 0.157 7932 Planarity : 0.004 0.044 9594 Dihedral : 6.607 67.684 7656 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.16 % Allowed : 12.82 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.10), residues: 6702 helix: 2.45 (0.10), residues: 2742 sheet: 0.97 (0.15), residues: 1080 loop : -0.99 (0.10), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 466 HIS 0.004 0.001 HIS C1045 PHE 0.025 0.001 PHE F1046 TYR 0.014 0.001 TYR A 582 ARG 0.010 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1197 time to evaluate : 5.893 Fit side-chains revert: symmetry clash REVERT: A 290 GLU cc_start: 0.8616 (pm20) cc_final: 0.8327 (pm20) REVERT: A 377 GLU cc_start: 0.8267 (tt0) cc_final: 0.8014 (tt0) REVERT: A 434 MET cc_start: 0.8852 (ttm) cc_final: 0.8626 (mtp) REVERT: A 448 THR cc_start: 0.8571 (m) cc_final: 0.8083 (m) REVERT: B 113 SER cc_start: 0.8572 (t) cc_final: 0.8358 (p) REVERT: B 290 GLU cc_start: 0.8603 (pm20) cc_final: 0.8314 (pm20) REVERT: B 377 GLU cc_start: 0.8269 (tt0) cc_final: 0.8013 (tt0) REVERT: B 448 THR cc_start: 0.8564 (m) cc_final: 0.8097 (m) REVERT: C 801 GLU cc_start: 0.8926 (tp30) cc_final: 0.8665 (mm-30) REVERT: D 118 MET cc_start: 0.8782 (mmp) cc_final: 0.8246 (mmt) REVERT: F 190 LEU cc_start: 0.9029 (tp) cc_final: 0.8786 (tp) REVERT: F 1069 MET cc_start: 0.8430 (ttp) cc_final: 0.8226 (ttp) outliers start: 64 outliers final: 32 residues processed: 1209 average time/residue: 2.0491 time to fit residues: 2996.1452 Evaluate side-chains 1216 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 1184 time to evaluate : 5.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 1209 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 920 THR Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 527 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 621 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 367 optimal weight: 3.9990 chunk 470 optimal weight: 0.0000 chunk 364 optimal weight: 5.9990 chunk 542 optimal weight: 2.9990 chunk 359 optimal weight: 0.5980 chunk 641 optimal weight: 5.9990 chunk 401 optimal weight: 2.9990 chunk 391 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 404 HIS B 404 HIS B 424 ASN B 799 GLN B1096 ASN C 404 HIS C 424 ASN C 944 ASN D 349 ASN D 404 HIS D 799 GLN D1213 GLN E 292 GLN E 404 HIS E 799 GLN E 944 ASN ** E1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS F 944 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1096 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 53700 Z= 0.199 Angle : 0.509 9.846 72816 Z= 0.265 Chirality : 0.043 0.159 7932 Planarity : 0.004 0.045 9594 Dihedral : 6.639 67.841 7656 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.85 % Allowed : 13.28 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.10), residues: 6702 helix: 2.43 (0.10), residues: 2778 sheet: 0.97 (0.15), residues: 1074 loop : -0.95 (0.10), residues: 2850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 466 HIS 0.005 0.001 HIS E 643 PHE 0.027 0.001 PHE F1046 TYR 0.014 0.001 TYR C 761 ARG 0.010 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1239 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 1192 time to evaluate : 5.850 Fit side-chains revert: symmetry clash REVERT: A 290 GLU cc_start: 0.8642 (pm20) cc_final: 0.8346 (pm20) REVERT: A 377 GLU cc_start: 0.8278 (tt0) cc_final: 0.8027 (tt0) REVERT: A 434 MET cc_start: 0.8876 (ttm) cc_final: 0.8592 (mtp) REVERT: B 113 SER cc_start: 0.8620 (t) cc_final: 0.8392 (p) REVERT: B 290 GLU cc_start: 0.8625 (pm20) cc_final: 0.8325 (pm20) REVERT: B 377 GLU cc_start: 0.8277 (tt0) cc_final: 0.8024 (tt0) REVERT: C 801 GLU cc_start: 0.8933 (tp30) cc_final: 0.8678 (mm-30) REVERT: C 1069 MET cc_start: 0.8498 (ttp) cc_final: 0.8292 (ttp) REVERT: D 118 MET cc_start: 0.8776 (mmp) cc_final: 0.8220 (mmt) REVERT: F 190 LEU cc_start: 0.9033 (tp) cc_final: 0.8804 (tp) outliers start: 47 outliers final: 38 residues processed: 1203 average time/residue: 2.0835 time to fit residues: 3021.1946 Evaluate side-chains 1224 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 1186 time to evaluate : 5.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 880 TRP Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 880 TRP Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1187 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 1175 GLN Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 920 THR Chi-restraints excluded: chain E residue 1175 GLN Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 494 GLU Chi-restraints excluded: chain F residue 527 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 397 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 383 optimal weight: 0.8980 chunk 193 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 408 optimal weight: 0.1980 chunk 437 optimal weight: 1.9990 chunk 317 optimal weight: 0.1980 chunk 59 optimal weight: 4.9990 chunk 504 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 404 HIS B 404 HIS B 424 ASN C 404 HIS C 424 ASN C 944 ASN C1096 ASN D 349 ASN D 404 HIS D 799 GLN E 292 GLN E 404 HIS E 799 GLN F 404 HIS F 786 ASN F 944 ASN F1096 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 53700 Z= 0.152 Angle : 0.482 9.675 72816 Z= 0.249 Chirality : 0.042 0.156 7932 Planarity : 0.004 0.044 9594 Dihedral : 6.505 67.678 7656 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.85 % Allowed : 13.37 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.10), residues: 6702 helix: 2.60 (0.10), residues: 2742 sheet: 0.98 (0.16), residues: 1014 loop : -0.83 (0.10), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 466 HIS 0.004 0.001 HIS C 267 PHE 0.025 0.001 PHE F1046 TYR 0.012 0.001 TYR B 582 ARG 0.010 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 1200 time to evaluate : 5.981 Fit side-chains revert: symmetry clash REVERT: A 290 GLU cc_start: 0.8622 (pm20) cc_final: 0.8332 (pm20) REVERT: A 377 GLU cc_start: 0.8269 (tt0) cc_final: 0.8012 (tt0) REVERT: A 434 MET cc_start: 0.8848 (ttm) cc_final: 0.8634 (mtp) REVERT: A 448 THR cc_start: 0.8469 (m) cc_final: 0.7982 (m) REVERT: B 113 SER cc_start: 0.8598 (t) cc_final: 0.8380 (p) REVERT: B 290 GLU cc_start: 0.8605 (pm20) cc_final: 0.8312 (pm20) REVERT: B 377 GLU cc_start: 0.8258 (tt0) cc_final: 0.8000 (tt0) REVERT: B 448 THR cc_start: 0.8475 (m) cc_final: 0.7986 (m) REVERT: C 801 GLU cc_start: 0.8918 (tp30) cc_final: 0.8707 (mm-30) REVERT: D 118 MET cc_start: 0.8775 (mmp) cc_final: 0.8223 (mmt) REVERT: F 190 LEU cc_start: 0.9025 (tp) cc_final: 0.8783 (tp) REVERT: F 1069 MET cc_start: 0.8396 (ttp) cc_final: 0.8194 (ttp) outliers start: 47 outliers final: 36 residues processed: 1206 average time/residue: 2.0800 time to fit residues: 3030.4627 Evaluate side-chains 1212 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 1176 time to evaluate : 5.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 1187 LYS Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 1175 GLN Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 920 THR Chi-restraints excluded: chain E residue 1175 GLN Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 494 GLU Chi-restraints excluded: chain F residue 527 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 583 optimal weight: 5.9990 chunk 614 optimal weight: 3.9990 chunk 561 optimal weight: 0.9980 chunk 598 optimal weight: 4.9990 chunk 360 optimal weight: 0.5980 chunk 260 optimal weight: 0.8980 chunk 469 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 540 optimal weight: 0.8980 chunk 565 optimal weight: 8.9990 chunk 596 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 404 HIS B 404 HIS B 424 ASN B1096 ASN C 404 HIS C 424 ASN C 677 ASN C 786 ASN C 944 ASN C1096 ASN D 404 HIS D 799 GLN E 292 GLN E 404 HIS E 799 GLN E 818 GLN F 404 HIS F 944 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 53700 Z= 0.178 Angle : 0.498 10.020 72816 Z= 0.258 Chirality : 0.043 0.153 7932 Planarity : 0.004 0.044 9594 Dihedral : 6.533 68.255 7656 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.92 % Allowed : 13.67 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.10), residues: 6702 helix: 2.54 (0.10), residues: 2778 sheet: 0.99 (0.16), residues: 1014 loop : -0.80 (0.10), residues: 2910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 466 HIS 0.005 0.001 HIS E 643 PHE 0.025 0.001 PHE B1046 TYR 0.012 0.001 TYR C 761 ARG 0.010 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 1184 time to evaluate : 5.944 Fit side-chains revert: symmetry clash REVERT: A 290 GLU cc_start: 0.8637 (pm20) cc_final: 0.8341 (pm20) REVERT: A 377 GLU cc_start: 0.8272 (tt0) cc_final: 0.8016 (tt0) REVERT: A 434 MET cc_start: 0.8869 (ttm) cc_final: 0.8649 (mtp) REVERT: A 448 THR cc_start: 0.8553 (m) cc_final: 0.8100 (m) REVERT: B 113 SER cc_start: 0.8617 (t) cc_final: 0.8390 (p) REVERT: B 290 GLU cc_start: 0.8617 (pm20) cc_final: 0.8317 (pm20) REVERT: B 377 GLU cc_start: 0.8260 (tt0) cc_final: 0.8003 (tt0) REVERT: B 448 THR cc_start: 0.8550 (m) cc_final: 0.8096 (m) REVERT: C 801 GLU cc_start: 0.8917 (tp30) cc_final: 0.8701 (mm-30) REVERT: D 118 MET cc_start: 0.8774 (mmp) cc_final: 0.8195 (mmt) REVERT: F 190 LEU cc_start: 0.9031 (tp) cc_final: 0.8800 (tp) outliers start: 51 outliers final: 41 residues processed: 1191 average time/residue: 2.1088 time to fit residues: 3029.4575 Evaluate side-chains 1219 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 1178 time to evaluate : 5.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 1187 LYS Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 1209 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 1175 GLN Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 920 THR Chi-restraints excluded: chain E residue 1175 GLN Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 247 MET Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 494 GLU Chi-restraints excluded: chain F residue 527 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 392 optimal weight: 4.9990 chunk 632 optimal weight: 4.9990 chunk 386 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 439 optimal weight: 0.0770 chunk 663 optimal weight: 2.9990 chunk 610 optimal weight: 0.0040 chunk 528 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 408 optimal weight: 1.9990 chunk 323 optimal weight: 0.7980 overall best weight: 0.6552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 404 HIS A1027 GLN B 404 HIS B 424 ASN C 404 HIS C 424 ASN C 944 ASN C1096 ASN D 404 HIS D 799 GLN E 292 GLN E 404 HIS E 799 GLN E1027 GLN F 404 HIS F 944 ASN F1027 GLN F1096 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 53700 Z= 0.154 Angle : 0.490 9.979 72816 Z= 0.253 Chirality : 0.042 0.153 7932 Planarity : 0.004 0.043 9594 Dihedral : 6.464 68.223 7656 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.87 % Allowed : 13.87 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.10), residues: 6702 helix: 2.65 (0.10), residues: 2742 sheet: 1.01 (0.16), residues: 1020 loop : -0.77 (0.10), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 466 HIS 0.004 0.001 HIS D 643 PHE 0.024 0.001 PHE F1046 TYR 0.012 0.001 TYR F 582 ARG 0.011 0.000 ARG A 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 1188 time to evaluate : 5.546 Fit side-chains revert: symmetry clash REVERT: A 290 GLU cc_start: 0.8627 (pm20) cc_final: 0.8334 (pm20) REVERT: A 377 GLU cc_start: 0.8267 (tt0) cc_final: 0.8009 (tt0) REVERT: A 434 MET cc_start: 0.8848 (ttm) cc_final: 0.8629 (mtp) REVERT: A 448 THR cc_start: 0.8467 (m) cc_final: 0.7982 (m) REVERT: B 113 SER cc_start: 0.8602 (t) cc_final: 0.8384 (p) REVERT: B 290 GLU cc_start: 0.8606 (pm20) cc_final: 0.8311 (pm20) REVERT: B 377 GLU cc_start: 0.8245 (tt0) cc_final: 0.7990 (tt0) REVERT: B 448 THR cc_start: 0.8462 (m) cc_final: 0.7975 (m) REVERT: C 801 GLU cc_start: 0.8904 (tp30) cc_final: 0.8690 (mm-30) REVERT: C 1069 MET cc_start: 0.8510 (ttp) cc_final: 0.8307 (ttp) REVERT: D 118 MET cc_start: 0.8775 (mmp) cc_final: 0.8199 (mmt) REVERT: F 190 LEU cc_start: 0.9028 (tp) cc_final: 0.8782 (tp) REVERT: F 1069 MET cc_start: 0.8397 (ttp) cc_final: 0.8180 (ttp) outliers start: 48 outliers final: 38 residues processed: 1194 average time/residue: 2.0643 time to fit residues: 2987.2544 Evaluate side-chains 1219 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 1181 time to evaluate : 5.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 826 LYS Chi-restraints excluded: chain B residue 1187 LYS Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain C residue 1209 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 1175 GLN Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 920 THR Chi-restraints excluded: chain E residue 1175 GLN Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 527 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 419 optimal weight: 5.9990 chunk 562 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 487 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 529 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 543 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 97 optimal weight: 0.0470 overall best weight: 1.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 404 HIS ** A1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 424 ASN B1096 ASN C 404 HIS C 424 ASN C 677 ASN C 845 GLN C 944 ASN C1096 ASN D 404 HIS D 799 GLN E 292 GLN E 404 HIS F 404 HIS F 590 HIS F 944 ASN F1096 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.111752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.101530 restraints weight = 69355.644| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.24 r_work: 0.3405 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 53700 Z= 0.338 Angle : 0.582 10.885 72816 Z= 0.304 Chirality : 0.047 0.162 7932 Planarity : 0.005 0.048 9594 Dihedral : 6.807 70.010 7656 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.83 % Allowed : 14.11 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.10), residues: 6702 helix: 2.30 (0.10), residues: 2784 sheet: 0.92 (0.16), residues: 1002 loop : -0.92 (0.10), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 970 HIS 0.009 0.001 HIS F 267 PHE 0.031 0.002 PHE B1046 TYR 0.021 0.002 TYR F 761 ARG 0.011 0.001 ARG A 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37901.31 seconds wall clock time: 794 minutes 24.72 seconds (47664.72 seconds total)