Starting phenix.real_space_refine on Tue Jun 24 22:57:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvk_34130/06_2025/7yvk_34130.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvk_34130/06_2025/7yvk_34130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvk_34130/06_2025/7yvk_34130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvk_34130/06_2025/7yvk_34130.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvk_34130/06_2025/7yvk_34130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvk_34130/06_2025/7yvk_34130.cif" } resolution = 3.2 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= -0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 18441 2.51 5 N 4710 2.21 5 O 5535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 2.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28809 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7725 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "C" Number of atoms: 7725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7725 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "B" Number of atoms: 7725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7725 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 796 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 796 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "N" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 796 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 18.13, per 1000 atoms: 0.63 Number of scatterers: 28809 At special positions: 0 Unit cell: (192.7, 168.1, 182.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 123 16.00 O 5535 8.00 N 4710 7.00 C 18441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.07 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.06 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.07 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 97 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.65 Conformation dependent library (CDL) restraints added in 3.6 seconds 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6996 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 58 sheets defined 20.5% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.896A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.695A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.539A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.506A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.826A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.989A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.681A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.034A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.981A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.006A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.633A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.823A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.554A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.510A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.962A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.648A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.229A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.005A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.829A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.601A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.785A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.622A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.634A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.529A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.760A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.010A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.597A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.075A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.876A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.811A pdb=" N THR H 92 " --> pdb=" O PRO H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.549A pdb=" N ASP I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 92 removed outlier: 3.720A pdb=" N THR K 92 " --> pdb=" O PRO K 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'N' and resid 88 through 92 removed outlier: 3.627A pdb=" N THR N 92 " --> pdb=" O PRO N 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 85 removed outlier: 3.666A pdb=" N ASP O 85 " --> pdb=" O ALA O 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.545A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.524A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.585A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.864A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.085A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.473A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.103A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.199A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.852A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.852A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.479A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.959A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.472A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.771A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.464A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.901A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.825A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.067A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.011A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.965A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.776A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.776A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.408A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 788 through 789 removed outlier: 6.041A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.621A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 29 through 31 removed outlier: 8.382A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.882A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.779A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.043A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.817A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 391 through 392 removed outlier: 4.058A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.011A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.662A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.662A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 735 through 736 removed outlier: 3.548A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.708A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE7, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.402A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 9 through 10 removed outlier: 6.624A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 9 through 10 Processing sheet with id=AF1, first strand: chain 'I' and resid 18 through 20 Processing sheet with id=AF2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AF4, first strand: chain 'K' and resid 59 through 61 removed outlier: 5.743A pdb=" N TRP K 49 " --> pdb=" O ARG K 40 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ARG K 40 " --> pdb=" O TRP K 49 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA K 51 " --> pdb=" O TRP K 38 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR K 95 " --> pdb=" O THR K 113 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR K 113 " --> pdb=" O TYR K 95 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.934A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AF7, first strand: chain 'L' and resid 18 through 20 Processing sheet with id=AF8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AG1, first strand: chain 'N' and resid 59 through 61 removed outlier: 5.342A pdb=" N TRP N 49 " --> pdb=" O ARG N 40 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG N 40 " --> pdb=" O TRP N 49 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA N 51 " --> pdb=" O TRP N 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 9 through 10 removed outlier: 6.919A pdb=" N TRP O 37 " --> pdb=" O MET O 49 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 9 through 10 Processing sheet with id=AG4, first strand: chain 'O' and resid 18 through 20 1150 hydrogen bonds defined for protein. 3042 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: 13.30 Time building geometry restraints manager: 7.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5697 1.32 - 1.46: 10531 1.46 - 1.59: 13109 1.59 - 1.73: 8 1.73 - 1.87: 145 Bond restraints: 29490 Sorted by residual: bond pdb=" C PRO B 863 " pdb=" O PRO B 863 " ideal model delta sigma weight residual 1.233 1.185 0.048 1.12e-02 7.97e+03 1.81e+01 bond pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " ideal model delta sigma weight residual 1.808 1.674 0.134 3.30e-02 9.18e+02 1.65e+01 bond pdb=" CB CYS A 760 " pdb=" SG CYS A 760 " ideal model delta sigma weight residual 1.808 1.679 0.129 3.30e-02 9.18e+02 1.52e+01 bond pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " ideal model delta sigma weight residual 1.808 1.680 0.128 3.30e-02 9.18e+02 1.52e+01 bond pdb=" CB TRP B 886 " pdb=" CG TRP B 886 " ideal model delta sigma weight residual 1.498 1.384 0.114 3.10e-02 1.04e+03 1.36e+01 ... (remaining 29485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 39728 4.22 - 8.44: 513 8.44 - 12.65: 33 12.65 - 16.87: 9 16.87 - 21.09: 1 Bond angle restraints: 40284 Sorted by residual: angle pdb=" C VAL O 53 " pdb=" N SER O 54 " pdb=" CA SER O 54 " ideal model delta sigma weight residual 121.58 107.92 13.66 1.95e+00 2.63e-01 4.91e+01 angle pdb=" CA CYS C 738 " pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " ideal model delta sigma weight residual 114.40 129.22 -14.82 2.30e+00 1.89e-01 4.15e+01 angle pdb=" C VAL L 53 " pdb=" N SER L 54 " pdb=" CA SER L 54 " ideal model delta sigma weight residual 121.58 109.19 12.39 1.95e+00 2.63e-01 4.03e+01 angle pdb=" CA CYS A 590 " pdb=" CB CYS A 590 " pdb=" SG CYS A 590 " ideal model delta sigma weight residual 114.40 128.64 -14.24 2.30e+00 1.89e-01 3.83e+01 angle pdb=" C ILE C 332 " pdb=" N THR C 333 " pdb=" CA THR C 333 " ideal model delta sigma weight residual 121.80 134.75 -12.95 2.16e+00 2.14e-01 3.60e+01 ... (remaining 40279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 16330 17.53 - 35.05: 1185 35.05 - 52.58: 267 52.58 - 70.10: 79 70.10 - 87.63: 19 Dihedral angle restraints: 17880 sinusoidal: 6987 harmonic: 10893 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 174.00 -81.00 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 171.16 -78.16 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -161.57 75.57 1 1.00e+01 1.00e-02 7.21e+01 ... (remaining 17877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3817 0.098 - 0.196: 833 0.196 - 0.294: 73 0.294 - 0.392: 9 0.392 - 0.490: 5 Chirality restraints: 4737 Sorted by residual: chirality pdb=" CA PHE C 855 " pdb=" N PHE C 855 " pdb=" C PHE C 855 " pdb=" CB PHE C 855 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CA CYS A 760 " pdb=" N CYS A 760 " pdb=" C CYS A 760 " pdb=" CB CYS A 760 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 ... (remaining 4734 not shown) Planarity restraints: 5127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE K 102 " 0.070 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO K 103 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO K 103 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO K 103 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE N 102 " 0.069 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO N 103 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO N 103 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO N 103 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE H 102 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.65e+01 pdb=" N PRO H 103 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.056 5.00e-02 4.00e+02 ... (remaining 5124 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 479 2.63 - 3.20: 26596 3.20 - 3.77: 41240 3.77 - 4.33: 55621 4.33 - 4.90: 96888 Nonbonded interactions: 220824 Sorted by model distance: nonbonded pdb=" NH2 ARG L 56 " pdb=" O SER L 61 " model vdw 2.063 3.120 nonbonded pdb=" O ILE H 105 " pdb=" OH TYR I 38 " model vdw 2.102 3.040 nonbonded pdb=" O TRP A 353 " pdb=" NH1 ARG A 466 " model vdw 2.116 3.120 nonbonded pdb=" O TRP C 353 " pdb=" NH1 ARG C 466 " model vdw 2.128 3.120 nonbonded pdb=" OG SER A 366 " pdb=" ND2 ASN A 388 " model vdw 2.136 3.120 ... (remaining 220819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 1146 or resid 1301 through 1311)) selection = (chain 'B' and (resid 27 through 1146 or resid 1301 through 1311)) selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } 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: 12.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.350 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 67.710 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.017 0.142 29535 Z= 0.682 Angle : 1.327 21.090 40374 Z= 0.722 Chirality : 0.079 0.490 4737 Planarity : 0.008 0.107 5127 Dihedral : 13.294 87.631 10749 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.47 % Favored : 94.20 % Rotamer: Outliers : 1.23 % Allowed : 8.86 % Favored : 89.92 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.12), residues: 3690 helix: 0.05 (0.19), residues: 665 sheet: -1.85 (0.14), residues: 1035 loop : -2.43 (0.12), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.005 TRP A 64 HIS 0.019 0.003 HIS B1048 PHE 0.052 0.005 PHE B 92 TYR 0.046 0.004 TYR A 170 ARG 0.016 0.002 ARG B 328 Details of bonding type rmsd hydrogen bonds : bond 0.15660 ( 1104) hydrogen bonds : angle 7.42013 ( 3042) SS BOND : bond 0.01366 ( 45) SS BOND : angle 5.32541 ( 90) covalent geometry : bond 0.01666 (29490) covalent geometry : angle 1.30431 (40284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 218 GLN cc_start: 0.8078 (mt0) cc_final: 0.7245 (tm-30) REVERT: C 237 ARG cc_start: 0.7763 (mtp180) cc_final: 0.7072 (ptt-90) REVERT: C 355 ARG cc_start: 0.7497 (tpt170) cc_final: 0.7127 (tpp80) REVERT: C 488 CYS cc_start: -0.0698 (OUTLIER) cc_final: -0.1096 (m) REVERT: B 237 ARG cc_start: 0.7353 (mtp180) cc_final: 0.6923 (ptm160) REVERT: B 238 PHE cc_start: 0.6411 (p90) cc_final: 0.6087 (p90) REVERT: B 354 ASN cc_start: 0.8285 (t0) cc_final: 0.7660 (t0) REVERT: B 403 ARG cc_start: 0.6504 (ttm-80) cc_final: 0.5350 (ttm-80) REVERT: B 488 CYS cc_start: 0.3973 (OUTLIER) cc_final: 0.3608 (t) REVERT: B 983 ARG cc_start: 0.6896 (mtm110) cc_final: 0.6519 (mtm110) REVERT: H 39 ILE cc_start: 0.6962 (mt) cc_final: 0.6620 (mm) REVERT: H 40 ARG cc_start: 0.8531 (ptt180) cc_final: 0.7689 (ttp80) REVERT: H 47 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.6972 (mm) REVERT: H 74 ASP cc_start: 0.8598 (t0) cc_final: 0.8397 (t0) REVERT: I 39 GLN cc_start: 0.6889 (tm-30) cc_final: 0.6650 (tt0) REVERT: I 49 MET cc_start: 0.6828 (mmp) cc_final: 0.6623 (mmm) REVERT: N 4 LEU cc_start: 0.3207 (OUTLIER) cc_final: 0.1958 (tt) REVERT: O 49 MET cc_start: 0.2954 (tpp) cc_final: 0.2209 (ttt) outliers start: 37 outliers final: 10 residues processed: 279 average time/residue: 0.4257 time to fit residues: 186.8440 Evaluate side-chains 188 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 21 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 0.9980 chunk 279 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 289 optimal weight: 5.9990 chunk 111 optimal weight: 0.0980 chunk 175 optimal weight: 0.1980 chunk 215 optimal weight: 8.9990 chunk 335 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS A 709 ASN A 762 GLN A 955 ASN A1088 HIS C 218 GLN C 481 ASN ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN C 856 ASN B 188 ASN B 417 ASN B 532 ASN B 657 ASN B 762 GLN B 978 ASN B1088 HIS B1134 ASN H 78 ASN H 111 GLN I 39 GLN K 78 ASN L 33 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.165268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.101548 restraints weight = 52549.203| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.24 r_work: 0.3329 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29535 Z= 0.146 Angle : 0.679 11.489 40374 Z= 0.354 Chirality : 0.047 0.229 4737 Planarity : 0.005 0.074 5127 Dihedral : 6.801 58.966 4774 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.88 % Favored : 95.04 % Rotamer: Outliers : 2.19 % Allowed : 10.78 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.58 (0.13), residues: 3690 helix: 1.40 (0.21), residues: 654 sheet: -0.83 (0.15), residues: 1028 loop : -2.08 (0.12), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 436 HIS 0.003 0.001 HIS C1088 PHE 0.016 0.001 PHE C 970 TYR 0.021 0.001 TYR A1138 ARG 0.010 0.001 ARG C 452 Details of bonding type rmsd hydrogen bonds : bond 0.05961 ( 1104) hydrogen bonds : angle 5.87805 ( 3042) SS BOND : bond 0.00823 ( 45) SS BOND : angle 2.62455 ( 90) covalent geometry : bond 0.00316 (29490) covalent geometry : angle 0.66814 (40284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 224 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.8299 (m-30) cc_final: 0.7823 (t0) REVERT: A 983 ARG cc_start: 0.8979 (ptm-80) cc_final: 0.8600 (ptm160) REVERT: C 218 GLN cc_start: 0.8678 (mt0) cc_final: 0.7482 (tm-30) REVERT: C 237 ARG cc_start: 0.8375 (mtp180) cc_final: 0.7083 (ptt-90) REVERT: C 355 ARG cc_start: 0.7459 (tpt170) cc_final: 0.7243 (tpp80) REVERT: C 960 ASN cc_start: 0.8897 (t0) cc_final: 0.8597 (t0) REVERT: C 994 ASP cc_start: 0.8558 (m-30) cc_final: 0.8289 (t0) REVERT: B 200 TYR cc_start: 0.8114 (m-80) cc_final: 0.7900 (m-80) REVERT: B 237 ARG cc_start: 0.7224 (mtp180) cc_final: 0.6888 (ptm160) REVERT: B 354 ASN cc_start: 0.8351 (t0) cc_final: 0.8099 (m-40) REVERT: B 403 ARG cc_start: 0.6440 (ttm-80) cc_final: 0.5166 (ttm-80) REVERT: B 409 GLN cc_start: 0.8451 (mt0) cc_final: 0.8230 (mt0) REVERT: B 525 CYS cc_start: 0.6065 (OUTLIER) cc_final: 0.5417 (m) REVERT: B 983 ARG cc_start: 0.7663 (mtm110) cc_final: 0.7205 (mtm110) REVERT: H 24 PHE cc_start: 0.8131 (p90) cc_final: 0.7639 (p90) REVERT: H 40 ARG cc_start: 0.8299 (ptt180) cc_final: 0.7533 (ttp-110) REVERT: I 39 GLN cc_start: 0.7003 (tm130) cc_final: 0.6473 (tt0) REVERT: I 49 MET cc_start: 0.7044 (mmp) cc_final: 0.6821 (mmp) REVERT: I 56 ARG cc_start: 0.8733 (tmm-80) cc_final: 0.8435 (tmm-80) REVERT: I 81 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7200 (pt0) REVERT: O 49 MET cc_start: 0.2973 (tpp) cc_final: 0.2297 (ttt) outliers start: 66 outliers final: 32 residues processed: 279 average time/residue: 0.4515 time to fit residues: 209.3024 Evaluate side-chains 203 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain N residue 21 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 354 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 128 optimal weight: 0.2980 chunk 141 optimal weight: 3.9990 chunk 287 optimal weight: 0.8980 chunk 296 optimal weight: 3.9990 chunk 121 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 394 ASN A 801 ASN A1005 GLN A1074 ASN A1134 ASN ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 ASN C1074 ASN C1134 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1074 ASN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.159514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.095802 restraints weight = 53151.965| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.04 r_work: 0.3259 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29535 Z= 0.203 Angle : 0.665 10.319 40374 Z= 0.347 Chirality : 0.047 0.358 4737 Planarity : 0.005 0.061 5127 Dihedral : 6.230 55.200 4762 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.66 % Rotamer: Outliers : 2.95 % Allowed : 12.44 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.20 (0.13), residues: 3690 helix: 1.63 (0.21), residues: 665 sheet: -0.61 (0.15), residues: 1008 loop : -1.80 (0.12), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 436 HIS 0.004 0.001 HIS B1058 PHE 0.022 0.002 PHE B 168 TYR 0.025 0.002 TYR A1138 ARG 0.003 0.000 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.06098 ( 1104) hydrogen bonds : angle 5.62251 ( 3042) SS BOND : bond 0.00608 ( 45) SS BOND : angle 2.43853 ( 90) covalent geometry : bond 0.00489 (29490) covalent geometry : angle 0.65611 (40284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 171 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.8373 (m-30) cc_final: 0.7855 (t0) REVERT: A 983 ARG cc_start: 0.9016 (ptm-80) cc_final: 0.8600 (ptm160) REVERT: C 218 GLN cc_start: 0.8707 (mt0) cc_final: 0.7445 (tm-30) REVERT: C 237 ARG cc_start: 0.8519 (mtp180) cc_final: 0.7219 (ptt-90) REVERT: C 355 ARG cc_start: 0.7434 (tpt170) cc_final: 0.7199 (tpp80) REVERT: C 702 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8617 (tp30) REVERT: C 960 ASN cc_start: 0.8955 (t0) cc_final: 0.8667 (t0) REVERT: B 200 TYR cc_start: 0.8122 (m-80) cc_final: 0.7915 (m-80) REVERT: B 237 ARG cc_start: 0.7190 (mtp180) cc_final: 0.6828 (ptm160) REVERT: B 403 ARG cc_start: 0.6545 (ttm-80) cc_final: 0.5252 (ttm-80) REVERT: B 406 GLU cc_start: 0.8163 (tp30) cc_final: 0.7743 (tp30) REVERT: B 455 LEU cc_start: 0.8678 (tp) cc_final: 0.8124 (tt) REVERT: B 493 GLN cc_start: 0.6470 (mp10) cc_final: 0.5866 (mp10) REVERT: B 791 THR cc_start: 0.7771 (OUTLIER) cc_final: 0.7443 (t) REVERT: B 886 TRP cc_start: 0.8272 (OUTLIER) cc_final: 0.7863 (m-90) REVERT: B 902 MET cc_start: 0.8808 (mmm) cc_final: 0.8482 (tpt) REVERT: H 40 ARG cc_start: 0.8264 (ptt180) cc_final: 0.7383 (ttp80) REVERT: H 56 ASP cc_start: 0.7758 (t0) cc_final: 0.7525 (t0) REVERT: I 49 MET cc_start: 0.7329 (mmp) cc_final: 0.7014 (mmm) REVERT: I 56 ARG cc_start: 0.8760 (tmm-80) cc_final: 0.7639 (ttm170) REVERT: I 62 ASN cc_start: 0.8283 (p0) cc_final: 0.7377 (p0) REVERT: I 81 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7254 (pt0) REVERT: O 49 MET cc_start: 0.2884 (tpp) cc_final: 0.2134 (ttt) outliers start: 89 outliers final: 60 residues processed: 253 average time/residue: 0.3716 time to fit residues: 157.0357 Evaluate side-chains 219 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 156 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain O residue 95 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 283 optimal weight: 0.4980 chunk 294 optimal weight: 0.9980 chunk 337 optimal weight: 8.9990 chunk 203 optimal weight: 3.9990 chunk 239 optimal weight: 8.9990 chunk 146 optimal weight: 0.0570 chunk 153 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 ASN C 856 ASN H 78 ASN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.164439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.100550 restraints weight = 52649.933| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.22 r_work: 0.3327 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 29535 Z= 0.119 Angle : 0.573 11.614 40374 Z= 0.298 Chirality : 0.044 0.302 4737 Planarity : 0.004 0.054 5127 Dihedral : 5.533 52.993 4760 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.88 % Favored : 95.07 % Rotamer: Outliers : 2.45 % Allowed : 14.33 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.84 (0.13), residues: 3690 helix: 2.01 (0.21), residues: 656 sheet: -0.27 (0.15), residues: 1032 loop : -1.66 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 436 HIS 0.002 0.000 HIS B1048 PHE 0.014 0.001 PHE B 168 TYR 0.021 0.001 TYR B1067 ARG 0.002 0.000 ARG I 56 Details of bonding type rmsd hydrogen bonds : bond 0.04735 ( 1104) hydrogen bonds : angle 5.26209 ( 3042) SS BOND : bond 0.00810 ( 45) SS BOND : angle 1.98011 ( 90) covalent geometry : bond 0.00265 (29490) covalent geometry : angle 0.56644 (40284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 190 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.8330 (m-30) cc_final: 0.7874 (t0) REVERT: A 983 ARG cc_start: 0.8966 (ptm-80) cc_final: 0.8569 (ptm160) REVERT: C 218 GLN cc_start: 0.8661 (mt0) cc_final: 0.7450 (tm-30) REVERT: C 237 ARG cc_start: 0.8445 (mtp180) cc_final: 0.7179 (ptt-90) REVERT: C 702 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8593 (tp30) REVERT: C 752 LEU cc_start: 0.9365 (tt) cc_final: 0.8989 (mp) REVERT: C 902 MET cc_start: 0.8878 (mmm) cc_final: 0.8523 (mmt) REVERT: C 960 ASN cc_start: 0.8853 (t0) cc_final: 0.8581 (t0) REVERT: B 329 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8384 (m-10) REVERT: B 403 ARG cc_start: 0.6617 (ttm-80) cc_final: 0.5347 (ttm-80) REVERT: B 406 GLU cc_start: 0.8106 (tp30) cc_final: 0.7667 (tp30) REVERT: B 455 LEU cc_start: 0.8638 (tp) cc_final: 0.8128 (tt) REVERT: B 465 GLU cc_start: 0.8374 (tt0) cc_final: 0.8165 (tt0) REVERT: B 493 GLN cc_start: 0.6613 (mp10) cc_final: 0.6019 (mp10) REVERT: B 619 GLU cc_start: 0.8843 (pt0) cc_final: 0.8456 (pt0) REVERT: B 886 TRP cc_start: 0.8069 (OUTLIER) cc_final: 0.7827 (m-90) REVERT: H 56 ASP cc_start: 0.7945 (t0) cc_final: 0.7689 (t0) REVERT: I 56 ARG cc_start: 0.8811 (tmm-80) cc_final: 0.7648 (ttm170) REVERT: I 62 ASN cc_start: 0.8284 (p0) cc_final: 0.7351 (p0) REVERT: I 81 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7200 (pt0) REVERT: K 71 ILE cc_start: 0.2226 (OUTLIER) cc_final: 0.1642 (mp) REVERT: N 65 LEU cc_start: 0.4353 (OUTLIER) cc_final: 0.4148 (pp) REVERT: O 49 MET cc_start: 0.3061 (tpp) cc_final: 0.2381 (ttt) outliers start: 74 outliers final: 45 residues processed: 254 average time/residue: 0.3822 time to fit residues: 161.0916 Evaluate side-chains 219 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 169 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 35 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 159 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 207 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 305 optimal weight: 0.0770 chunk 238 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 265 optimal weight: 0.0270 chunk 294 optimal weight: 2.9990 chunk 12 optimal weight: 0.0000 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 ASN ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN B 762 GLN H 78 ASN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.163246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.102229 restraints weight = 53068.273| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.50 r_work: 0.3354 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 29535 Z= 0.102 Angle : 0.545 9.913 40374 Z= 0.283 Chirality : 0.043 0.185 4737 Planarity : 0.004 0.047 5127 Dihedral : 5.045 53.431 4757 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.80 % Favored : 95.15 % Rotamer: Outliers : 2.69 % Allowed : 14.79 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.57 (0.13), residues: 3690 helix: 2.15 (0.21), residues: 658 sheet: 0.03 (0.15), residues: 1029 loop : -1.54 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 258 HIS 0.002 0.000 HIS A 69 PHE 0.017 0.001 PHE C 392 TYR 0.020 0.001 TYR B1067 ARG 0.003 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 1104) hydrogen bonds : angle 5.04639 ( 3042) SS BOND : bond 0.00472 ( 45) SS BOND : angle 1.77276 ( 90) covalent geometry : bond 0.00218 (29490) covalent geometry : angle 0.53931 (40284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 179 time to evaluate : 3.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.8317 (m-30) cc_final: 0.7896 (t0) REVERT: A 983 ARG cc_start: 0.8898 (ptm-80) cc_final: 0.8517 (ptm160) REVERT: C 218 GLN cc_start: 0.8535 (mt0) cc_final: 0.7470 (tm-30) REVERT: C 237 ARG cc_start: 0.8236 (mtp180) cc_final: 0.7009 (ptt-90) REVERT: C 752 LEU cc_start: 0.9360 (tt) cc_final: 0.9016 (mp) REVERT: C 902 MET cc_start: 0.8700 (mmm) cc_final: 0.8332 (mmt) REVERT: C 960 ASN cc_start: 0.8700 (t0) cc_final: 0.8439 (t0) REVERT: B 329 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8047 (m-10) REVERT: B 403 ARG cc_start: 0.6640 (ttm-80) cc_final: 0.5403 (ttm-80) REVERT: B 455 LEU cc_start: 0.8678 (tp) cc_final: 0.8179 (tt) REVERT: B 465 GLU cc_start: 0.8236 (tt0) cc_final: 0.8032 (tt0) REVERT: B 493 GLN cc_start: 0.6651 (mp10) cc_final: 0.6048 (mp10) REVERT: B 619 GLU cc_start: 0.8738 (pt0) cc_final: 0.8287 (pp20) REVERT: B 752 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8982 (tt) REVERT: H 56 ASP cc_start: 0.7975 (t0) cc_final: 0.7722 (t0) REVERT: H 60 ARG cc_start: 0.5800 (mmt180) cc_final: 0.5597 (mmt180) REVERT: I 56 ARG cc_start: 0.8812 (tmm-80) cc_final: 0.7965 (ttp-170) REVERT: I 62 ASN cc_start: 0.8261 (p0) cc_final: 0.7583 (p0) REVERT: I 64 PHE cc_start: 0.7641 (m-80) cc_final: 0.7220 (m-80) REVERT: I 81 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7242 (pt0) REVERT: I 84 ASP cc_start: 0.7168 (m-30) cc_final: 0.6461 (m-30) REVERT: O 49 MET cc_start: 0.3158 (tpp) cc_final: 0.2487 (ttt) outliers start: 81 outliers final: 58 residues processed: 251 average time/residue: 0.3855 time to fit residues: 161.1280 Evaluate side-chains 223 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 163 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 35 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 11 optimal weight: 0.0570 chunk 18 optimal weight: 20.0000 chunk 364 optimal weight: 0.0870 chunk 278 optimal weight: 1.9990 chunk 355 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 316 optimal weight: 0.0000 chunk 214 optimal weight: 0.9980 chunk 329 optimal weight: 50.0000 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN H 78 ASN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.162676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.101105 restraints weight = 53336.829| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.94 r_work: 0.3370 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 29535 Z= 0.110 Angle : 0.548 13.908 40374 Z= 0.283 Chirality : 0.043 0.219 4737 Planarity : 0.004 0.047 5127 Dihedral : 4.824 53.786 4757 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % Rotamer: Outliers : 2.69 % Allowed : 15.12 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.43 (0.14), residues: 3690 helix: 2.28 (0.21), residues: 654 sheet: 0.17 (0.16), residues: 1020 loop : -1.47 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 436 HIS 0.002 0.000 HIS A1064 PHE 0.014 0.001 PHE A 135 TYR 0.020 0.001 TYR B1067 ARG 0.002 0.000 ARG C1000 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 1104) hydrogen bonds : angle 5.00826 ( 3042) SS BOND : bond 0.00575 ( 45) SS BOND : angle 1.82796 ( 90) covalent geometry : bond 0.00246 (29490) covalent geometry : angle 0.54197 (40284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 172 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.8346 (m-30) cc_final: 0.7951 (t0) REVERT: A 983 ARG cc_start: 0.8987 (ptm-80) cc_final: 0.8557 (ptt90) REVERT: C 218 GLN cc_start: 0.8627 (mt0) cc_final: 0.7505 (tm-30) REVERT: C 237 ARG cc_start: 0.8448 (mtp180) cc_final: 0.7154 (ptt-90) REVERT: C 752 LEU cc_start: 0.9352 (tt) cc_final: 0.9023 (mp) REVERT: C 902 MET cc_start: 0.8916 (mmm) cc_final: 0.8624 (mmt) REVERT: C 960 ASN cc_start: 0.8852 (t0) cc_final: 0.8595 (t0) REVERT: B 329 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7844 (m-10) REVERT: B 403 ARG cc_start: 0.6656 (ttm-80) cc_final: 0.5406 (ttm-80) REVERT: B 455 LEU cc_start: 0.8713 (tp) cc_final: 0.8243 (tt) REVERT: B 465 GLU cc_start: 0.8319 (tt0) cc_final: 0.7995 (mt-10) REVERT: B 493 GLN cc_start: 0.6628 (mp10) cc_final: 0.6003 (mp10) REVERT: B 619 GLU cc_start: 0.8873 (pt0) cc_final: 0.8409 (pp20) REVERT: B 752 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8951 (tt) REVERT: H 56 ASP cc_start: 0.8050 (t0) cc_final: 0.7770 (t0) REVERT: I 56 ARG cc_start: 0.8847 (tmm-80) cc_final: 0.8231 (tmm-80) REVERT: I 62 ASN cc_start: 0.8294 (p0) cc_final: 0.7957 (p0) REVERT: I 84 ASP cc_start: 0.7125 (m-30) cc_final: 0.6468 (m-30) REVERT: O 49 MET cc_start: 0.3138 (tpp) cc_final: 0.2473 (ttt) outliers start: 81 outliers final: 62 residues processed: 243 average time/residue: 0.3672 time to fit residues: 148.5461 Evaluate side-chains 226 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 162 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 35 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 206 optimal weight: 6.9990 chunk 285 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 315 optimal weight: 0.0670 chunk 95 optimal weight: 0.8980 chunk 327 optimal weight: 30.0000 chunk 120 optimal weight: 30.0000 chunk 27 optimal weight: 0.0570 chunk 101 optimal weight: 3.9990 chunk 284 optimal weight: 0.6980 chunk 52 optimal weight: 0.1980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN C 901 GLN C1074 ASN H 78 ASN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.162217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.099245 restraints weight = 52928.011| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.08 r_work: 0.3409 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 29535 Z= 0.098 Angle : 0.529 13.707 40374 Z= 0.273 Chirality : 0.043 0.242 4737 Planarity : 0.004 0.047 5127 Dihedral : 4.545 53.057 4757 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 2.29 % Allowed : 16.09 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.25 (0.14), residues: 3690 helix: 2.35 (0.21), residues: 655 sheet: 0.31 (0.15), residues: 1072 loop : -1.38 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 436 HIS 0.002 0.000 HIS C1088 PHE 0.016 0.001 PHE H 24 TYR 0.020 0.001 TYR B1067 ARG 0.003 0.000 ARG C1000 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 1104) hydrogen bonds : angle 4.82079 ( 3042) SS BOND : bond 0.00470 ( 45) SS BOND : angle 1.70312 ( 90) covalent geometry : bond 0.00210 (29490) covalent geometry : angle 0.52387 (40284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 186 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.8323 (m-30) cc_final: 0.7896 (t0) REVERT: A 983 ARG cc_start: 0.8994 (ptm-80) cc_final: 0.8696 (ptm-80) REVERT: C 218 GLN cc_start: 0.8620 (mt0) cc_final: 0.7537 (tm-30) REVERT: C 237 ARG cc_start: 0.8414 (mtp180) cc_final: 0.7174 (ptt-90) REVERT: C 752 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9052 (mp) REVERT: C 902 MET cc_start: 0.8859 (mmm) cc_final: 0.8607 (mmt) REVERT: C 960 ASN cc_start: 0.8819 (t0) cc_final: 0.8566 (t0) REVERT: B 329 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.7253 (m-10) REVERT: B 403 ARG cc_start: 0.6687 (ttm-80) cc_final: 0.5454 (ttm-80) REVERT: B 406 GLU cc_start: 0.7706 (tp30) cc_final: 0.7261 (mm-30) REVERT: B 409 GLN cc_start: 0.8784 (mt0) cc_final: 0.8331 (mt0) REVERT: B 455 LEU cc_start: 0.8740 (tp) cc_final: 0.8270 (tt) REVERT: B 465 GLU cc_start: 0.8233 (tt0) cc_final: 0.7933 (mt-10) REVERT: B 493 GLN cc_start: 0.6811 (mp10) cc_final: 0.6185 (mp10) REVERT: B 720 ILE cc_start: 0.8665 (pp) cc_final: 0.8415 (pp) REVERT: B 752 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8928 (tt) REVERT: I 56 ARG cc_start: 0.8808 (tmm-80) cc_final: 0.8185 (tmm-80) REVERT: I 62 ASN cc_start: 0.8265 (p0) cc_final: 0.7899 (p0) REVERT: I 81 GLN cc_start: 0.7928 (pt0) cc_final: 0.7714 (pm20) REVERT: I 84 ASP cc_start: 0.6986 (m-30) cc_final: 0.6369 (m-30) REVERT: K 102 ILE cc_start: 0.3681 (mm) cc_final: 0.3216 (tp) outliers start: 69 outliers final: 56 residues processed: 247 average time/residue: 0.4045 time to fit residues: 165.0284 Evaluate side-chains 233 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 174 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 35 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 212 optimal weight: 3.9990 chunk 319 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 175 optimal weight: 0.0470 chunk 320 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 188 optimal weight: 3.9990 chunk 294 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 901 GLN B 774 GLN H 78 ASN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.159997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.097042 restraints weight = 53184.205| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.55 r_work: 0.3317 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 29535 Z= 0.129 Angle : 0.558 13.750 40374 Z= 0.286 Chirality : 0.044 0.245 4737 Planarity : 0.004 0.048 5127 Dihedral : 4.595 54.451 4756 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.28 % Rotamer: Outliers : 2.26 % Allowed : 16.55 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.22 (0.14), residues: 3690 helix: 2.38 (0.21), residues: 653 sheet: 0.28 (0.16), residues: 1054 loop : -1.32 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 436 HIS 0.002 0.001 HIS C1064 PHE 0.013 0.001 PHE C 238 TYR 0.022 0.001 TYR B1067 ARG 0.004 0.000 ARG B 498 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 1104) hydrogen bonds : angle 4.94520 ( 3042) SS BOND : bond 0.00501 ( 45) SS BOND : angle 1.85012 ( 90) covalent geometry : bond 0.00304 (29490) covalent geometry : angle 0.55192 (40284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 174 time to evaluate : 3.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.8329 (m-30) cc_final: 0.8034 (t0) REVERT: A 983 ARG cc_start: 0.8863 (ptm-80) cc_final: 0.8496 (ptt90) REVERT: C 218 GLN cc_start: 0.8571 (mt0) cc_final: 0.7531 (tm-30) REVERT: C 237 ARG cc_start: 0.8290 (mtp180) cc_final: 0.7061 (ptt-90) REVERT: C 752 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9030 (mp) REVERT: C 960 ASN cc_start: 0.8804 (t0) cc_final: 0.8563 (t0) REVERT: B 329 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.7521 (m-10) REVERT: B 403 ARG cc_start: 0.6665 (ttm-80) cc_final: 0.5393 (ttm-80) REVERT: B 455 LEU cc_start: 0.8790 (tp) cc_final: 0.8293 (tt) REVERT: B 465 GLU cc_start: 0.8179 (tt0) cc_final: 0.7918 (mt-10) REVERT: B 493 GLN cc_start: 0.6863 (mp10) cc_final: 0.6197 (mp10) REVERT: B 752 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8915 (tt) REVERT: I 56 ARG cc_start: 0.8835 (tmm-80) cc_final: 0.8049 (ttp-170) REVERT: I 62 ASN cc_start: 0.8258 (p0) cc_final: 0.7542 (p0) REVERT: I 64 PHE cc_start: 0.7705 (m-80) cc_final: 0.7258 (m-80) REVERT: I 81 GLN cc_start: 0.7998 (pt0) cc_final: 0.7793 (pm20) REVERT: I 84 ASP cc_start: 0.6942 (m-30) cc_final: 0.6264 (m-30) REVERT: K 102 ILE cc_start: 0.3487 (mm) cc_final: 0.3056 (tp) outliers start: 68 outliers final: 60 residues processed: 234 average time/residue: 0.4182 time to fit residues: 159.4520 Evaluate side-chains 226 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 163 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 35 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 127 optimal weight: 0.9980 chunk 210 optimal weight: 6.9990 chunk 217 optimal weight: 0.9980 chunk 15 optimal weight: 0.0020 chunk 237 optimal weight: 2.9990 chunk 320 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 323 optimal weight: 7.9990 chunk 270 optimal weight: 1.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN H 78 ASN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.158613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.094448 restraints weight = 52846.740| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.12 r_work: 0.3327 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 29535 Z= 0.159 Angle : 0.580 13.705 40374 Z= 0.300 Chirality : 0.045 0.246 4737 Planarity : 0.004 0.048 5127 Dihedral : 4.798 54.460 4756 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.28 % Rotamer: Outliers : 2.45 % Allowed : 16.45 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.29 (0.14), residues: 3690 helix: 2.27 (0.21), residues: 650 sheet: 0.18 (0.16), residues: 1034 loop : -1.28 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 436 HIS 0.003 0.001 HIS C1083 PHE 0.023 0.001 PHE B 201 TYR 0.023 0.001 TYR I 51 ARG 0.003 0.000 ARG C 905 Details of bonding type rmsd hydrogen bonds : bond 0.05040 ( 1104) hydrogen bonds : angle 5.08015 ( 3042) SS BOND : bond 0.00561 ( 45) SS BOND : angle 1.98693 ( 90) covalent geometry : bond 0.00380 (29490) covalent geometry : angle 0.57327 (40284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 167 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.8383 (m-30) cc_final: 0.8030 (t0) REVERT: A 983 ARG cc_start: 0.9027 (ptm-80) cc_final: 0.8644 (ptt90) REVERT: C 91 TYR cc_start: 0.8923 (t80) cc_final: 0.8677 (t80) REVERT: C 218 GLN cc_start: 0.8658 (mt0) cc_final: 0.7575 (tm-30) REVERT: C 237 ARG cc_start: 0.8489 (mtp180) cc_final: 0.7226 (ptt-90) REVERT: C 752 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9055 (mp) REVERT: C 902 MET cc_start: 0.8907 (mmm) cc_final: 0.8659 (mmt) REVERT: C 960 ASN cc_start: 0.8929 (t0) cc_final: 0.8678 (t0) REVERT: C 1002 GLN cc_start: 0.8835 (tt0) cc_final: 0.8604 (tp40) REVERT: B 329 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.7799 (m-10) REVERT: B 403 ARG cc_start: 0.6718 (ttm-80) cc_final: 0.5466 (ttm-80) REVERT: B 455 LEU cc_start: 0.8755 (tp) cc_final: 0.8241 (tt) REVERT: B 465 GLU cc_start: 0.8330 (tt0) cc_final: 0.7961 (mt-10) REVERT: B 493 GLN cc_start: 0.6781 (mp10) cc_final: 0.6110 (mp10) REVERT: B 752 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8950 (tt) REVERT: B 791 THR cc_start: 0.7906 (OUTLIER) cc_final: 0.7585 (t) REVERT: H 40 ARG cc_start: 0.8466 (ptt180) cc_final: 0.8078 (ptt-90) REVERT: I 56 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8036 (ttp-170) REVERT: I 62 ASN cc_start: 0.8319 (p0) cc_final: 0.7539 (p0) REVERT: I 64 PHE cc_start: 0.7620 (m-80) cc_final: 0.7139 (m-80) REVERT: I 84 ASP cc_start: 0.6844 (m-30) cc_final: 0.6193 (m-30) REVERT: K 102 ILE cc_start: 0.3555 (mm) cc_final: 0.3053 (tp) outliers start: 74 outliers final: 63 residues processed: 230 average time/residue: 0.4026 time to fit residues: 152.9599 Evaluate side-chains 231 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 163 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 343 optimal weight: 5.9990 chunk 345 optimal weight: 40.0000 chunk 35 optimal weight: 0.4980 chunk 261 optimal weight: 0.9990 chunk 332 optimal weight: 6.9990 chunk 164 optimal weight: 0.7980 chunk 226 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 286 optimal weight: 2.9990 chunk 230 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN H 78 ASN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.163186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.100915 restraints weight = 52860.239| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.49 r_work: 0.3319 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 29535 Z= 0.114 Angle : 0.556 13.328 40374 Z= 0.285 Chirality : 0.044 0.295 4737 Planarity : 0.004 0.048 5127 Dihedral : 4.639 53.592 4756 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.61 % Favored : 95.34 % Rotamer: Outliers : 2.06 % Allowed : 17.11 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.17 (0.14), residues: 3690 helix: 2.32 (0.21), residues: 658 sheet: 0.29 (0.16), residues: 1056 loop : -1.24 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 436 HIS 0.002 0.001 HIS C1088 PHE 0.023 0.001 PHE B 201 TYR 0.022 0.001 TYR B1067 ARG 0.011 0.000 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 1104) hydrogen bonds : angle 4.94368 ( 3042) SS BOND : bond 0.00483 ( 45) SS BOND : angle 1.77601 ( 90) covalent geometry : bond 0.00261 (29490) covalent geometry : angle 0.55010 (40284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 168 time to evaluate : 4.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8017 (tpt-90) cc_final: 0.7674 (mmt180) REVERT: A 979 ASP cc_start: 0.8278 (m-30) cc_final: 0.7966 (t0) REVERT: A 983 ARG cc_start: 0.8935 (ptm-80) cc_final: 0.8544 (ptt90) REVERT: C 91 TYR cc_start: 0.8831 (t80) cc_final: 0.8627 (t80) REVERT: C 218 GLN cc_start: 0.8575 (mt0) cc_final: 0.7547 (tm-30) REVERT: C 237 ARG cc_start: 0.8257 (mtp180) cc_final: 0.7047 (ptt-90) REVERT: C 752 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9039 (mp) REVERT: C 902 MET cc_start: 0.8778 (mmm) cc_final: 0.8528 (mmt) REVERT: C 960 ASN cc_start: 0.8775 (t0) cc_final: 0.8515 (t0) REVERT: C 1002 GLN cc_start: 0.8652 (tt0) cc_final: 0.8417 (tp40) REVERT: B 403 ARG cc_start: 0.6606 (ttm-80) cc_final: 0.5360 (ttm-80) REVERT: B 455 LEU cc_start: 0.8767 (tp) cc_final: 0.8230 (tt) REVERT: B 465 GLU cc_start: 0.8174 (tt0) cc_final: 0.7882 (mt-10) REVERT: B 493 GLN cc_start: 0.6728 (mp10) cc_final: 0.6058 (mp10) REVERT: B 752 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8908 (tt) REVERT: H 40 ARG cc_start: 0.8481 (ptt180) cc_final: 0.8058 (ptt-90) REVERT: I 56 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7995 (ttp-170) REVERT: I 62 ASN cc_start: 0.8322 (p0) cc_final: 0.7533 (p0) REVERT: I 64 PHE cc_start: 0.7540 (m-80) cc_final: 0.6944 (m-80) REVERT: I 84 ASP cc_start: 0.6683 (m-30) cc_final: 0.6247 (m-30) REVERT: K 102 ILE cc_start: 0.3271 (mm) cc_final: 0.2832 (tp) outliers start: 62 outliers final: 57 residues processed: 221 average time/residue: 0.4007 time to fit residues: 147.9650 Evaluate side-chains 222 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 162 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.3496 > 50: distance: 25 - 29: 3.133 distance: 29 - 30: 8.986 distance: 30 - 31: 4.205 distance: 30 - 33: 8.099 distance: 31 - 32: 9.895 distance: 31 - 34: 3.381 distance: 34 - 35: 13.118 distance: 35 - 36: 23.221 distance: 35 - 38: 27.005 distance: 36 - 37: 15.358 distance: 36 - 41: 9.992 distance: 38 - 39: 26.097 distance: 41 - 42: 10.490 distance: 42 - 43: 19.769 distance: 42 - 45: 13.808 distance: 43 - 44: 8.320 distance: 43 - 49: 10.229 distance: 45 - 46: 6.913 distance: 46 - 47: 13.602 distance: 46 - 48: 19.884 distance: 49 - 50: 5.825 distance: 49 - 174: 17.025 distance: 50 - 51: 7.875 distance: 51 - 52: 7.198 distance: 52 - 171: 6.682 distance: 54 - 55: 6.445 distance: 54 - 56: 3.627 distance: 55 - 57: 3.753 distance: 56 - 58: 3.084 distance: 57 - 58: 4.184 distance: 59 - 60: 4.326 distance: 60 - 61: 5.962 distance: 60 - 63: 7.801 distance: 61 - 62: 7.882 distance: 61 - 65: 6.766 distance: 63 - 64: 12.967 distance: 65 - 66: 6.656 distance: 65 - 156: 7.751 distance: 66 - 67: 4.569 distance: 66 - 69: 7.362 distance: 67 - 68: 5.146 distance: 67 - 72: 6.879 distance: 68 - 153: 9.210 distance: 69 - 71: 8.939 distance: 72 - 73: 6.506 distance: 73 - 74: 6.183 distance: 73 - 76: 16.385 distance: 74 - 77: 6.111 distance: 77 - 78: 4.313 distance: 77 - 143: 6.796 distance: 78 - 79: 3.641 distance: 78 - 81: 10.661 distance: 79 - 80: 5.409 distance: 82 - 83: 4.781 distance: 83 - 84: 3.345 distance: 84 - 85: 5.843 distance: 84 - 90: 4.507 distance: 86 - 87: 5.981 distance: 87 - 89: 10.046 distance: 91 - 92: 3.988 distance: 92 - 101: 3.094 distance: 93 - 127: 4.076 distance: 94 - 95: 5.096 distance: 96 - 98: 6.096 distance: 98 - 100: 3.349 distance: 99 - 100: 5.526