Starting phenix.real_space_refine on Mon Aug 25 15:04:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvk_34130/08_2025/7yvk_34130.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvk_34130/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/7yvk_34130/08_2025/7yvk_34130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvk_34130/08_2025/7yvk_34130.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yvk_34130/08_2025/7yvk_34130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvk_34130/08_2025/7yvk_34130.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 7, 'GLU:plan': 8, 'PHE:plan': 2, 'ARG:plan': 5, 'TYR:plan': 2} 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: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 7, 'GLU:plan': 8, 'PHE:plan': 2, 'ARG:plan': 5, 'TYR:plan': 2} 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: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 7, 'GLU:plan': 8, 'PHE:plan': 2, 'ARG:plan': 5, 'TYR:plan': 2} 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: 6.53, per 1000 atoms: 0.23 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: 2.59 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.7 microseconds 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: 0.90 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: 6.81 Time building geometry restraints manager: 3.51 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 1311) selection = (chain 'B' and resid 27 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: 12.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 27.040 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.120 ------------------------------------------------------------------------------- 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 : 12.73 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (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 ARG 0.016 0.002 ARG B 328 TYR 0.046 0.004 TYR A 170 PHE 0.052 0.005 PHE B 92 TRP 0.049 0.005 TRP A 64 HIS 0.019 0.003 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.01666 (29490) covalent geometry : angle 1.30431 (40284) SS BOND : bond 0.01366 ( 45) SS BOND : angle 5.32541 ( 90) hydrogen bonds : bond 0.15660 ( 1104) hydrogen bonds : angle 7.42013 ( 3042) *********************** 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 : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash 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: -0.1098 (m) REVERT: C 712 ILE cc_start: 0.8674 (mm) cc_final: 0.8474 (tt) REVERT: B 237 ARG cc_start: 0.7353 (mtp180) cc_final: 0.6946 (ptm160) REVERT: B 354 ASN cc_start: 0.8285 (t0) cc_final: 0.7661 (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: 0.3610 (t) REVERT: B 983 ARG cc_start: 0.6896 (mtm110) cc_final: 0.6518 (mtm110) REVERT: H 39 ILE cc_start: 0.6962 (mt) cc_final: 0.6622 (mm) REVERT: H 40 ARG cc_start: 0.8531 (ptt180) cc_final: 0.7688 (ttp80) REVERT: H 47 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.6981 (mm) REVERT: H 74 ASP cc_start: 0.8598 (t0) cc_final: 0.8397 (t0) 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: 0.2210 (ttt) outliers start: 37 outliers final: 10 residues processed: 279 average time/residue: 0.1656 time to fit residues: 72.2045 Evaluate side-chains 186 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN 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 C1088 HIS 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 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 = 0.4328 r_free = 0.4328 target = 0.164743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.100754 restraints weight = 52671.891| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.22 r_work: 0.3309 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29535 Z= 0.153 Angle : 0.680 11.256 40374 Z= 0.355 Chirality : 0.047 0.273 4737 Planarity : 0.005 0.076 5127 Dihedral : 6.727 59.935 4774 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.88 % Favored : 95.04 % Rotamer: Outliers : 2.35 % Allowed : 10.71 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.13), residues: 3690 helix: 1.40 (0.21), residues: 654 sheet: -0.84 (0.15), residues: 1025 loop : -2.08 (0.12), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 452 TYR 0.021 0.001 TYR A1138 PHE 0.022 0.001 PHE B 238 TRP 0.017 0.001 TRP C 436 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00344 (29490) covalent geometry : angle 0.66979 (40284) SS BOND : bond 0.00577 ( 45) SS BOND : angle 2.55856 ( 90) hydrogen bonds : bond 0.05973 ( 1104) hydrogen bonds : angle 5.85134 ( 3042) *********************** 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 293 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 222 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.8294 (m-30) cc_final: 0.7807 (t0) REVERT: A 983 ARG cc_start: 0.8978 (ptm-80) cc_final: 0.8588 (ptm160) REVERT: C 218 GLN cc_start: 0.8693 (mt0) cc_final: 0.7453 (tm-30) REVERT: C 237 ARG cc_start: 0.8364 (mtp180) cc_final: 0.7087 (ptt-90) REVERT: C 355 ARG cc_start: 0.7439 (tpt170) cc_final: 0.7239 (tpp80) REVERT: C 960 ASN cc_start: 0.8928 (t0) cc_final: 0.8617 (t0) REVERT: B 237 ARG cc_start: 0.7197 (mtp180) cc_final: 0.6837 (ptm160) REVERT: B 342 PHE cc_start: 0.8577 (m-10) cc_final: 0.8375 (m-10) REVERT: B 354 ASN cc_start: 0.8318 (t0) cc_final: 0.8078 (m-40) REVERT: B 403 ARG cc_start: 0.6461 (ttm-80) cc_final: 0.5327 (ttm-80) REVERT: B 525 CYS cc_start: 0.6128 (OUTLIER) cc_final: 0.5477 (m) REVERT: B 983 ARG cc_start: 0.7649 (mtm110) cc_final: 0.7171 (mtm110) REVERT: H 24 PHE cc_start: 0.8110 (p90) cc_final: 0.7607 (p90) REVERT: H 40 ARG cc_start: 0.8310 (ptt180) cc_final: 0.7572 (ttp-110) REVERT: I 56 ARG cc_start: 0.8705 (tmm-80) cc_final: 0.8391 (tmm-80) REVERT: I 81 GLN cc_start: 0.7477 (mm-40) cc_final: 0.7179 (pt0) REVERT: O 49 MET cc_start: 0.2964 (tpp) cc_final: 0.2284 (ttt) outliers start: 71 outliers final: 36 residues processed: 280 average time/residue: 0.1482 time to fit residues: 67.9291 Evaluate side-chains 211 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 720 ILE 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 1094 VAL 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 I residue 35 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain O residue 95 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 174 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 338 optimal weight: 30.0000 chunk 152 optimal weight: 0.2980 chunk 269 optimal weight: 3.9990 chunk 259 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 332 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 801 ASN A1074 ASN ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.162512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097991 restraints weight = 53008.569| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.24 r_work: 0.3265 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 29535 Z= 0.188 Angle : 0.654 12.100 40374 Z= 0.340 Chirality : 0.047 0.354 4737 Planarity : 0.005 0.063 5127 Dihedral : 6.165 54.906 4762 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.04 % Favored : 94.88 % Rotamer: Outliers : 2.99 % Allowed : 12.50 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.13), residues: 3690 helix: 1.66 (0.21), residues: 665 sheet: -0.63 (0.15), residues: 964 loop : -1.80 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 56 TYR 0.024 0.002 TYR A1138 PHE 0.022 0.002 PHE B 168 TRP 0.017 0.001 TRP C 436 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00453 (29490) covalent geometry : angle 0.64450 (40284) SS BOND : bond 0.00636 ( 45) SS BOND : angle 2.42489 ( 90) hydrogen bonds : bond 0.05935 ( 1104) hydrogen bonds : angle 5.58301 ( 3042) *********************** 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 264 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 174 time to evaluate : 0.692 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: 0.8369 (m-30) cc_final: 0.7862 (t0) REVERT: A 983 ARG cc_start: 0.9011 (ptm-80) cc_final: 0.8603 (ptm160) REVERT: C 218 GLN cc_start: 0.8722 (mt0) cc_final: 0.7452 (tm-30) REVERT: C 237 ARG cc_start: 0.8501 (mtp180) cc_final: 0.7241 (ptt-90) REVERT: C 355 ARG cc_start: 0.7498 (tpt170) cc_final: 0.7251 (tpp80) REVERT: C 702 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8570 (tp30) REVERT: C 960 ASN cc_start: 0.8966 (t0) cc_final: 0.8685 (t0) REVERT: C 1002 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8426 (tm-30) REVERT: B 237 ARG cc_start: 0.7181 (mtp180) cc_final: 0.6808 (ptm160) REVERT: B 403 ARG cc_start: 0.6636 (ttm-80) cc_final: 0.5390 (ttm-80) REVERT: B 453 TYR cc_start: 0.7659 (p90) cc_final: 0.6824 (p90) REVERT: B 455 LEU cc_start: 0.8634 (tp) cc_final: 0.8097 (tt) REVERT: B 493 GLN cc_start: 0.6524 (mp10) cc_final: 0.5959 (mp10) REVERT: B 619 GLU cc_start: 0.8930 (pt0) cc_final: 0.8596 (pt0) REVERT: B 791 THR cc_start: 0.7742 (OUTLIER) cc_final: 0.7420 (t) REVERT: B 886 TRP cc_start: 0.8216 (OUTLIER) cc_final: 0.7828 (m-90) REVERT: B 902 MET cc_start: 0.8799 (mmm) cc_final: 0.8503 (tpt) REVERT: I 56 ARG cc_start: 0.8729 (tmm-80) cc_final: 0.7590 (ttm170) REVERT: I 62 ASN cc_start: 0.8248 (p0) cc_final: 0.7360 (p0) REVERT: I 64 PHE cc_start: 0.7756 (m-80) cc_final: 0.7153 (m-80) REVERT: I 81 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7277 (pt0) REVERT: O 49 MET cc_start: 0.2996 (tpp) cc_final: 0.2233 (ttt) outliers start: 90 outliers final: 57 residues processed: 254 average time/residue: 0.1392 time to fit residues: 59.1287 Evaluate side-chains 215 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 155 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 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 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 590 CYS 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 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 994 ASP 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 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 754 LEU 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 293 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 276 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 chunk 349 optimal weight: 30.0000 chunk 325 optimal weight: 20.0000 chunk 156 optimal weight: 0.5980 chunk 312 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** C 856 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4301 r_free = 0.4301 target = 0.160335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.096897 restraints weight = 52958.618| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.02 r_work: 0.3285 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29535 Z= 0.153 Angle : 0.598 11.735 40374 Z= 0.311 Chirality : 0.045 0.311 4737 Planarity : 0.004 0.055 5127 Dihedral : 5.694 53.955 4760 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.99 % Favored : 94.96 % Rotamer: Outliers : 2.82 % Allowed : 14.76 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.13), residues: 3690 helix: 1.91 (0.21), residues: 656 sheet: -0.29 (0.15), residues: 994 loop : -1.66 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 56 TYR 0.022 0.001 TYR B1067 PHE 0.016 0.001 PHE B 238 TRP 0.017 0.001 TRP C 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00363 (29490) covalent geometry : angle 0.59051 (40284) SS BOND : bond 0.00644 ( 45) SS BOND : angle 2.09682 ( 90) hydrogen bonds : bond 0.05309 ( 1104) hydrogen bonds : angle 5.36341 ( 3042) *********************** 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 262 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 177 time to evaluate : 0.844 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: 0.8331 (m-30) cc_final: 0.7842 (t0) REVERT: A 983 ARG cc_start: 0.9027 (ptm-80) cc_final: 0.8625 (ptm160) REVERT: C 218 GLN cc_start: 0.8694 (mt0) cc_final: 0.7482 (tm-30) REVERT: C 237 ARG cc_start: 0.8498 (mtp180) cc_final: 0.7197 (ptt-90) REVERT: C 702 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8673 (tp30) REVERT: C 902 MET cc_start: 0.8908 (mmm) cc_final: 0.8540 (mmt) REVERT: C 960 ASN cc_start: 0.8929 (t0) cc_final: 0.8661 (t0) REVERT: C 1002 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8239 (tm-30) REVERT: B 237 ARG cc_start: 0.7160 (mtp180) cc_final: 0.6828 (ptm160) REVERT: B 329 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8525 (m-10) REVERT: B 403 ARG cc_start: 0.6686 (ttm-80) cc_final: 0.5452 (ttm-80) REVERT: B 453 TYR cc_start: 0.7622 (p90) cc_final: 0.6761 (p90) REVERT: B 455 LEU cc_start: 0.8629 (tp) cc_final: 0.8023 (tt) REVERT: B 456 PHE cc_start: 0.8359 (m-80) cc_final: 0.8089 (m-80) REVERT: B 465 GLU cc_start: 0.8380 (tt0) cc_final: 0.8164 (tt0) REVERT: B 493 GLN cc_start: 0.6570 (mp10) cc_final: 0.5995 (mp10) REVERT: B 619 GLU cc_start: 0.8925 (pt0) cc_final: 0.8581 (pt0) REVERT: B 886 TRP cc_start: 0.8141 (m-90) cc_final: 0.7834 (m-90) REVERT: B 902 MET cc_start: 0.8799 (mmm) cc_final: 0.8465 (tpt) REVERT: H 40 ARG cc_start: 0.8315 (ptt180) cc_final: 0.7361 (ttp80) REVERT: I 56 ARG cc_start: 0.8793 (tmm-80) cc_final: 0.7626 (ttm170) REVERT: I 62 ASN cc_start: 0.8241 (p0) cc_final: 0.7312 (p0) REVERT: I 81 GLN cc_start: 0.7464 (mm-40) cc_final: 0.7129 (pt0) REVERT: I 84 ASP cc_start: 0.7147 (m-30) cc_final: 0.6471 (m-30) REVERT: K 71 ILE cc_start: 0.2093 (OUTLIER) cc_final: 0.1481 (mp) REVERT: O 49 MET cc_start: 0.3037 (tpp) cc_final: 0.2367 (ttt) outliers start: 85 outliers final: 59 residues processed: 251 average time/residue: 0.1540 time to fit residues: 63.6826 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 : 0.886 ------------------------------------------------------------------------------- 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 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 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 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 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 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE 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 398 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 887 THR 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 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 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 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 190 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 297 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 352 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 236 optimal weight: 0.7980 chunk 285 optimal weight: 0.7980 chunk 50 optimal weight: 0.0010 chunk 112 optimal weight: 5.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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** C 751 ASN ** B 616 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.161965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.100210 restraints weight = 52972.921| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.46 r_work: 0.3316 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 29535 Z= 0.117 Angle : 0.565 12.438 40374 Z= 0.293 Chirality : 0.044 0.273 4737 Planarity : 0.004 0.049 5127 Dihedral : 5.249 53.708 4757 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.09 % Favored : 94.85 % Rotamer: Outliers : 2.82 % Allowed : 15.22 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.13), residues: 3690 helix: 2.09 (0.21), residues: 656 sheet: -0.07 (0.15), residues: 1023 loop : -1.56 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1000 TYR 0.021 0.001 TYR B1067 PHE 0.015 0.001 PHE B 238 TRP 0.018 0.001 TRP C 436 HIS 0.002 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00265 (29490) covalent geometry : angle 0.55802 (40284) SS BOND : bond 0.00726 ( 45) SS BOND : angle 1.90064 ( 90) hydrogen bonds : bond 0.04639 ( 1104) hydrogen bonds : angle 5.16998 ( 3042) *********************** 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 265 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 180 time to evaluate : 0.907 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: 0.8328 (m-30) cc_final: 0.7981 (t0) REVERT: A 983 ARG cc_start: 0.8930 (ptm-80) cc_final: 0.8511 (ptt90) REVERT: C 218 GLN cc_start: 0.8590 (mt0) cc_final: 0.7485 (tm-30) REVERT: C 237 ARG cc_start: 0.8288 (mtp180) cc_final: 0.7068 (ptt-90) REVERT: C 752 LEU cc_start: 0.9362 (tt) cc_final: 0.9005 (mp) REVERT: C 902 MET cc_start: 0.8728 (mmm) cc_final: 0.8324 (mmt) REVERT: C 960 ASN cc_start: 0.8783 (t0) cc_final: 0.8534 (t0) REVERT: B 237 ARG cc_start: 0.7107 (mtp180) cc_final: 0.6800 (ptm160) REVERT: B 329 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8090 (m-10) REVERT: B 403 ARG cc_start: 0.6751 (ttm-80) cc_final: 0.5497 (ttm-80) REVERT: B 453 TYR cc_start: 0.7610 (p90) cc_final: 0.6808 (p90) REVERT: B 455 LEU cc_start: 0.8694 (tp) cc_final: 0.8049 (tt) REVERT: B 456 PHE cc_start: 0.8271 (m-80) cc_final: 0.8006 (m-80) REVERT: B 465 GLU cc_start: 0.8259 (tt0) cc_final: 0.8044 (tt0) REVERT: B 493 GLN cc_start: 0.6706 (mp10) cc_final: 0.6112 (mp10) REVERT: B 508 TYR cc_start: 0.7911 (m-80) cc_final: 0.7675 (m-80) REVERT: B 619 GLU cc_start: 0.8768 (pt0) cc_final: 0.8322 (pt0) REVERT: B 752 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8992 (tt) REVERT: H 40 ARG cc_start: 0.8375 (ptt180) cc_final: 0.7390 (ttp80) REVERT: I 37 TRP cc_start: 0.5192 (m100) cc_final: 0.4941 (m100) REVERT: I 56 ARG cc_start: 0.8803 (tmm-80) cc_final: 0.7641 (ttm170) REVERT: I 62 ASN cc_start: 0.8250 (p0) cc_final: 0.7339 (p0) REVERT: I 81 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7169 (pt0) REVERT: I 84 ASP cc_start: 0.7242 (m-30) cc_final: 0.6543 (m-30) REVERT: O 49 MET cc_start: 0.2990 (tpp) cc_final: 0.2374 (ttt) outliers start: 85 outliers final: 57 residues processed: 253 average time/residue: 0.1480 time to fit residues: 61.5917 Evaluate side-chains 226 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 167 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 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 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 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 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 738 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN 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 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 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 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 45 optimal weight: 9.9990 chunk 91 optimal weight: 0.3980 chunk 98 optimal weight: 0.6980 chunk 365 optimal weight: 30.0000 chunk 193 optimal weight: 3.9990 chunk 338 optimal weight: 40.0000 chunk 60 optimal weight: 6.9990 chunk 239 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 283 optimal weight: 1.9990 chunk 258 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** C1134 ASN ** B 616 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.160669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.098204 restraints weight = 53147.728| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.97 r_work: 0.3255 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2605 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= 0.146 Angle : 0.582 11.678 40374 Z= 0.301 Chirality : 0.045 0.289 4737 Planarity : 0.004 0.047 5127 Dihedral : 5.171 54.547 4757 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.80 % Favored : 95.15 % Rotamer: Outliers : 3.08 % Allowed : 15.22 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.13), residues: 3690 helix: 2.12 (0.21), residues: 655 sheet: 0.01 (0.15), residues: 1016 loop : -1.49 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 454 TYR 0.022 0.001 TYR B1067 PHE 0.014 0.001 PHE B 238 TRP 0.018 0.001 TRP C 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00348 (29490) covalent geometry : angle 0.57349 (40284) SS BOND : bond 0.00557 ( 45) SS BOND : angle 2.11973 ( 90) hydrogen bonds : bond 0.05043 ( 1104) hydrogen bonds : angle 5.17584 ( 3042) *********************** 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 261 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 168 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6246 (m-80) cc_final: 0.6041 (m-80) REVERT: A 902 MET cc_start: 0.8706 (tpt) cc_final: 0.8485 (mmt) REVERT: A 979 ASP cc_start: 0.8340 (m-30) cc_final: 0.7949 (t0) REVERT: A 983 ARG cc_start: 0.8955 (ptm-80) cc_final: 0.8542 (ptt90) REVERT: C 218 GLN cc_start: 0.8710 (mt0) cc_final: 0.7533 (tm-30) REVERT: C 237 ARG cc_start: 0.8500 (mtp180) cc_final: 0.7205 (ptt-90) REVERT: C 355 ARG cc_start: 0.7691 (tpt170) cc_final: 0.7426 (tpp80) REVERT: C 752 LEU cc_start: 0.9366 (tt) cc_final: 0.9003 (mp) REVERT: C 960 ASN cc_start: 0.8894 (t0) cc_final: 0.8634 (t0) REVERT: C 1002 GLN cc_start: 0.8943 (tt0) cc_final: 0.8517 (tm-30) REVERT: B 329 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8153 (m-10) REVERT: B 403 ARG cc_start: 0.6693 (ttm-80) cc_final: 0.5420 (ttm-80) REVERT: B 453 TYR cc_start: 0.7636 (p90) cc_final: 0.6783 (p90) REVERT: B 455 LEU cc_start: 0.8698 (tp) cc_final: 0.8002 (tt) REVERT: B 456 PHE cc_start: 0.8376 (m-80) cc_final: 0.8113 (m-80) REVERT: B 465 GLU cc_start: 0.8370 (tt0) cc_final: 0.8150 (tt0) REVERT: B 493 GLN cc_start: 0.6649 (mp10) cc_final: 0.6086 (mp10) REVERT: B 619 GLU cc_start: 0.8925 (pt0) cc_final: 0.8489 (pt0) REVERT: B 752 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8959 (tt) REVERT: H 40 ARG cc_start: 0.8377 (ptt180) cc_final: 0.7377 (ttp80) REVERT: I 49 MET cc_start: 0.6047 (mmp) cc_final: 0.5452 (mmp) REVERT: I 56 ARG cc_start: 0.8787 (tmm-80) cc_final: 0.7966 (ttp-170) REVERT: I 62 ASN cc_start: 0.8271 (p0) cc_final: 0.7604 (p0) REVERT: I 81 GLN cc_start: 0.7523 (mm-40) cc_final: 0.7322 (pt0) REVERT: I 84 ASP cc_start: 0.7171 (m-30) cc_final: 0.6507 (m-30) REVERT: O 49 MET cc_start: 0.2883 (tpp) cc_final: 0.2283 (ttt) outliers start: 93 outliers final: 74 residues processed: 249 average time/residue: 0.1442 time to fit residues: 59.0911 Evaluate side-chains 237 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 161 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 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 881 THR 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 A residue 1141 LEU 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 510 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 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1072 GLU 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 398 ASP Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 THR 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 859 THR 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 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 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 332 optimal weight: 7.9990 chunk 19 optimal weight: 0.0030 chunk 252 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 275 optimal weight: 0.0270 chunk 94 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 321 optimal weight: 6.9990 chunk 229 optimal weight: 0.1980 overall best weight: 0.4248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 ASN A 913 GLN C 801 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 = 0.4351 r_free = 0.4351 target = 0.162870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.101163 restraints weight = 53072.555| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.97 r_work: 0.3372 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 29535 Z= 0.101 Angle : 0.536 11.012 40374 Z= 0.277 Chirality : 0.043 0.249 4737 Planarity : 0.004 0.047 5127 Dihedral : 4.785 52.954 4757 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.72 % Favored : 95.23 % Rotamer: Outliers : 2.42 % Allowed : 16.25 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.14), residues: 3690 helix: 2.26 (0.21), residues: 660 sheet: 0.18 (0.15), residues: 1030 loop : -1.41 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1000 TYR 0.021 0.001 TYR I 51 PHE 0.022 0.001 PHE B 238 TRP 0.036 0.001 TRP I 37 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00220 (29490) covalent geometry : angle 0.53094 (40284) SS BOND : bond 0.00508 ( 45) SS BOND : angle 1.68019 ( 90) hydrogen bonds : bond 0.04098 ( 1104) hydrogen bonds : angle 4.94528 ( 3042) *********************** 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 247 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 174 time to evaluate : 0.741 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: 0.8339 (m-30) cc_final: 0.7984 (t0) REVERT: A 983 ARG cc_start: 0.9006 (ptm-80) cc_final: 0.8614 (ptt90) REVERT: C 218 GLN cc_start: 0.8636 (mt0) cc_final: 0.7569 (tm-30) REVERT: C 237 ARG cc_start: 0.8428 (mtp180) cc_final: 0.7170 (ptt-90) REVERT: C 752 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9043 (mp) REVERT: C 902 MET cc_start: 0.8934 (mmm) cc_final: 0.8710 (mmt) REVERT: C 960 ASN cc_start: 0.8864 (t0) cc_final: 0.8610 (t0) REVERT: B 273 ARG cc_start: 0.7287 (mmm160) cc_final: 0.6526 (mtm180) REVERT: B 403 ARG cc_start: 0.6708 (ttm-80) cc_final: 0.5472 (ttm-80) REVERT: B 453 TYR cc_start: 0.7645 (p90) cc_final: 0.6837 (p90) REVERT: B 455 LEU cc_start: 0.8746 (tp) cc_final: 0.8131 (tt) REVERT: B 456 PHE cc_start: 0.8317 (m-80) cc_final: 0.8083 (m-80) REVERT: B 465 GLU cc_start: 0.8282 (tt0) cc_final: 0.7970 (mt-10) REVERT: B 493 GLN cc_start: 0.6760 (mp10) cc_final: 0.6256 (mp10) REVERT: B 752 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8929 (tt) REVERT: I 47 LYS cc_start: 0.8070 (tttp) cc_final: 0.7388 (tmtt) REVERT: I 49 MET cc_start: 0.6529 (mmp) cc_final: 0.5152 (mmp) REVERT: I 56 ARG cc_start: 0.8798 (tmm-80) cc_final: 0.8201 (tmm-80) REVERT: I 62 ASN cc_start: 0.8283 (p0) cc_final: 0.7962 (p0) REVERT: I 64 PHE cc_start: 0.7785 (m-80) cc_final: 0.7563 (m-80) REVERT: I 84 ASP cc_start: 0.7158 (m-30) cc_final: 0.6460 (m-30) outliers start: 73 outliers final: 57 residues processed: 240 average time/residue: 0.1464 time to fit residues: 57.6568 Evaluate side-chains 223 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 164 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS 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 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 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 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 483 VAL 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 859 THR 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 76 optimal weight: 0.9990 chunk 172 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 359 optimal weight: 30.0000 chunk 19 optimal weight: 40.0000 chunk 248 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 270 optimal weight: 2.9990 chunk 311 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** B 616 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.161235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.099432 restraints weight = 53192.176| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.51 r_work: 0.3297 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29535 Z= 0.134 Angle : 0.557 11.844 40374 Z= 0.288 Chirality : 0.044 0.241 4737 Planarity : 0.004 0.048 5127 Dihedral : 4.789 54.566 4757 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.80 % Favored : 95.15 % Rotamer: Outliers : 2.72 % Allowed : 16.42 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.14), residues: 3690 helix: 2.26 (0.21), residues: 659 sheet: 0.24 (0.16), residues: 1010 loop : -1.36 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 63 TYR 0.023 0.001 TYR B1067 PHE 0.020 0.001 PHE B 238 TRP 0.015 0.001 TRP I 37 HIS 0.015 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00316 (29490) covalent geometry : angle 0.55055 (40284) SS BOND : bond 0.00578 ( 45) SS BOND : angle 1.82839 ( 90) hydrogen bonds : bond 0.04682 ( 1104) hydrogen bonds : angle 5.01530 ( 3042) *********************** 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 250 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 168 time to evaluate : 0.675 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: 0.8300 (m-30) cc_final: 0.7963 (t0) REVERT: A 983 ARG cc_start: 0.8915 (ptm-80) cc_final: 0.8524 (ptt90) REVERT: C 218 GLN cc_start: 0.8586 (mt0) cc_final: 0.7544 (tm-30) REVERT: C 237 ARG cc_start: 0.8317 (mtp180) cc_final: 0.7111 (ptt-90) REVERT: C 752 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9052 (mp) REVERT: C 960 ASN cc_start: 0.8771 (t0) cc_final: 0.8532 (t0) REVERT: B 403 ARG cc_start: 0.6689 (ttm-80) cc_final: 0.5418 (ttm-80) REVERT: B 453 TYR cc_start: 0.7676 (p90) cc_final: 0.6881 (p90) REVERT: B 455 LEU cc_start: 0.8763 (tp) cc_final: 0.8124 (tt) REVERT: B 456 PHE cc_start: 0.8297 (m-80) cc_final: 0.8040 (m-80) REVERT: B 465 GLU cc_start: 0.8191 (tt0) cc_final: 0.7947 (tt0) REVERT: B 493 GLN cc_start: 0.6882 (mp10) cc_final: 0.6360 (mp10) REVERT: B 752 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8943 (tt) REVERT: I 56 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8148 (tmm-80) REVERT: I 62 ASN cc_start: 0.8270 (p0) cc_final: 0.7929 (p0) REVERT: I 81 GLN cc_start: 0.7981 (pt0) cc_final: 0.7779 (pm20) REVERT: I 84 ASP cc_start: 0.7003 (m-30) cc_final: 0.6276 (m-30) outliers start: 82 outliers final: 69 residues processed: 237 average time/residue: 0.1515 time to fit residues: 59.3054 Evaluate side-chains 233 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 161 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 931 ILE 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 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 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 856 ASN Chi-restraints excluded: chain C residue 867 ASP 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 335 LEU Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL 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 763 LEU Chi-restraints excluded: chain B residue 791 THR 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 H residue 80 VAL 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 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 93 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 193 optimal weight: 0.0570 chunk 197 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 305 optimal weight: 0.5980 chunk 231 optimal weight: 0.0370 chunk 269 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 519 HIS 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 = 0.4350 r_free = 0.4350 target = 0.162642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.100878 restraints weight = 53224.611| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.97 r_work: 0.3375 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 29535 Z= 0.104 Angle : 0.531 12.081 40374 Z= 0.275 Chirality : 0.043 0.214 4737 Planarity : 0.004 0.047 5127 Dihedral : 4.586 53.187 4756 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 2.52 % Allowed : 16.98 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.14), residues: 3690 helix: 2.33 (0.21), residues: 659 sheet: 0.32 (0.15), residues: 1085 loop : -1.32 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1000 TYR 0.022 0.001 TYR B1067 PHE 0.019 0.001 PHE B 238 TRP 0.016 0.001 TRP I 37 HIS 0.012 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00233 (29490) covalent geometry : angle 0.52537 (40284) SS BOND : bond 0.00488 ( 45) SS BOND : angle 1.68015 ( 90) hydrogen bonds : bond 0.04071 ( 1104) hydrogen bonds : angle 4.87646 ( 3042) *********************** 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 246 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 170 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8052 (tpt-90) cc_final: 0.7772 (tpt90) REVERT: A 979 ASP cc_start: 0.8316 (m-30) cc_final: 0.7957 (t0) REVERT: A 983 ARG cc_start: 0.9016 (ptm-80) cc_final: 0.8632 (ptt90) REVERT: C 91 TYR cc_start: 0.8877 (t80) cc_final: 0.8609 (t80) REVERT: C 218 GLN cc_start: 0.8640 (mt0) cc_final: 0.7585 (tm-30) REVERT: C 237 ARG cc_start: 0.8386 (mtp180) cc_final: 0.7137 (ptt-90) REVERT: C 752 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9062 (mp) REVERT: C 960 ASN cc_start: 0.8819 (t0) cc_final: 0.8570 (t0) REVERT: B 329 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.7567 (m-10) REVERT: B 403 ARG cc_start: 0.6685 (ttm-80) cc_final: 0.5450 (ttm-80) REVERT: B 453 TYR cc_start: 0.7673 (p90) cc_final: 0.6852 (p90) REVERT: B 455 LEU cc_start: 0.8769 (tp) cc_final: 0.8142 (tt) REVERT: B 456 PHE cc_start: 0.8341 (m-80) cc_final: 0.8097 (m-80) REVERT: B 465 GLU cc_start: 0.8266 (tt0) cc_final: 0.7959 (mt-10) REVERT: B 493 GLN cc_start: 0.6839 (mp10) cc_final: 0.6317 (mp10) REVERT: B 752 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8905 (tt) REVERT: I 56 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8210 (tmm-80) REVERT: I 62 ASN cc_start: 0.8285 (p0) cc_final: 0.7934 (p0) REVERT: I 81 GLN cc_start: 0.7939 (pt0) cc_final: 0.7697 (pm20) REVERT: I 84 ASP cc_start: 0.6982 (m-30) cc_final: 0.6360 (m-30) REVERT: K 102 ILE cc_start: 0.3425 (mm) cc_final: 0.2973 (tp) outliers start: 76 outliers final: 65 residues processed: 239 average time/residue: 0.1499 time to fit residues: 59.2104 Evaluate side-chains 228 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 159 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 608 VAL 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 856 ASN 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 425 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL 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 763 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 H residue 80 VAL 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 ************** Weight determination summary: number of chunks: 369 random chunks: chunk 341 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 347 optimal weight: 7.9990 chunk 346 optimal weight: 7.9990 chunk 238 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 164 optimal weight: 0.5980 chunk 189 optimal weight: 0.6980 chunk 363 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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** H 78 ASN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.161750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.099181 restraints weight = 52723.385| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.57 r_work: 0.3291 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29535 Z= 0.147 Angle : 0.569 12.098 40374 Z= 0.294 Chirality : 0.044 0.226 4737 Planarity : 0.004 0.048 5127 Dihedral : 4.723 54.691 4756 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.28 % Rotamer: Outliers : 2.55 % Allowed : 17.18 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.14), residues: 3690 helix: 2.26 (0.21), residues: 658 sheet: 0.12 (0.16), residues: 1022 loop : -1.25 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 355 TYR 0.024 0.001 TYR B1067 PHE 0.020 0.001 PHE B 238 TRP 0.043 0.001 TRP C 353 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00352 (29490) covalent geometry : angle 0.56261 (40284) SS BOND : bond 0.00518 ( 45) SS BOND : angle 1.87060 ( 90) hydrogen bonds : bond 0.04829 ( 1104) hydrogen bonds : angle 5.03067 ( 3042) ********************** 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 241 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 164 time to evaluate : 1.063 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: 0.8322 (m-30) cc_final: 0.8017 (t0) REVERT: A 983 ARG cc_start: 0.8918 (ptm-80) cc_final: 0.8540 (ptt90) REVERT: C 218 GLN cc_start: 0.8579 (mt0) cc_final: 0.7514 (tm-30) REVERT: C 237 ARG cc_start: 0.8284 (mtp180) cc_final: 0.7075 (ptt-90) REVERT: C 752 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9008 (mp) REVERT: B 329 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.7744 (m-10) REVERT: B 403 ARG cc_start: 0.6651 (ttm-80) cc_final: 0.5408 (ttm-80) REVERT: B 453 TYR cc_start: 0.7631 (p90) cc_final: 0.6776 (p90) REVERT: B 455 LEU cc_start: 0.8748 (tp) cc_final: 0.8097 (tt) REVERT: B 465 GLU cc_start: 0.8137 (tt0) cc_final: 0.7824 (mt-10) REVERT: B 493 GLN cc_start: 0.6784 (mp10) cc_final: 0.6259 (mp10) REVERT: B 752 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8926 (tt) REVERT: I 56 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8308 (tmm-80) REVERT: I 62 ASN cc_start: 0.8251 (p0) cc_final: 0.7888 (p0) REVERT: I 84 ASP cc_start: 0.6899 (m-30) cc_final: 0.6248 (m-30) outliers start: 77 outliers final: 67 residues processed: 231 average time/residue: 0.1508 time to fit residues: 57.6439 Evaluate side-chains 229 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 158 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 501 TYR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 697 MET 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 A residue 1114 ILE 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 524 VAL Chi-restraints excluded: chain C residue 525 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 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1072 GLU 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 425 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL 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 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 858 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 H residue 80 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 295 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 210 optimal weight: 0.4980 chunk 328 optimal weight: 40.0000 chunk 128 optimal weight: 4.9990 chunk 262 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 276 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** H 78 ASN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.162098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.099127 restraints weight = 53103.779| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.04 r_work: 0.3339 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29535 Z= 0.130 Angle : 0.556 11.965 40374 Z= 0.288 Chirality : 0.044 0.217 4737 Planarity : 0.004 0.048 5127 Dihedral : 4.700 53.937 4756 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.77 % Favored : 95.18 % Rotamer: Outliers : 2.45 % Allowed : 17.35 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.14), residues: 3690 helix: 2.26 (0.21), residues: 658 sheet: 0.26 (0.16), residues: 1035 loop : -1.26 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 355 TYR 0.023 0.001 TYR B1067 PHE 0.020 0.001 PHE B 238 TRP 0.026 0.001 TRP C 436 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00305 (29490) covalent geometry : angle 0.54992 (40284) SS BOND : bond 0.00502 ( 45) SS BOND : angle 1.78156 ( 90) hydrogen bonds : bond 0.04610 ( 1104) hydrogen bonds : angle 4.98531 ( 3042) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10412.29 seconds wall clock time: 177 minutes 20.17 seconds (10640.17 seconds total)