Starting phenix.real_space_refine on Tue Aug 26 22:58:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hhz_34808/08_2025/8hhz_34808.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhz_34808/08_2025/8hhz_34808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hhz_34808/08_2025/8hhz_34808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhz_34808/08_2025/8hhz_34808.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hhz_34808/08_2025/8hhz_34808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhz_34808/08_2025/8hhz_34808.map" } resolution = 4.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 13578 atoms to isotropic. 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 122 5.16 5 C 20449 2.51 5 N 5291 2.21 5 O 6158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s 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: 32020 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7429 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 47, 'TRANS': 929} Chain breaks: 11 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 2, 'GLU:plan': 6, 'PHE:plan': 1, 'GLN:plan1': 6, 'TYR:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 124 Chain: "B" Number of atoms: 7424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7424 Classifications: {'peptide': 981} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 50, 'TRANS': 930} Chain breaks: 11 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 7, 'ASN:plan1': 2, 'GLU:plan': 6, 'PHE:plan': 1, 'GLN:plan1': 6, 'TYR:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 127 Chain: "C" Number of atoms: 7438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 7438 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 50, 'TRANS': 929} Chain breaks: 11 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 9, 'ASN:plan1': 5, 'GLU:plan': 7, 'PHE:plan': 2, 'ARG:plan': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 152 Chain: "E" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1650 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1593 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain: "G" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1650 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1593 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain: "I" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1650 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1593 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Time building chain proxies: 7.91, per 1000 atoms: 0.25 Number of scatterers: 32020 At special positions: 0 Unit cell: (191.86, 204.58, 184.44, 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 122 16.00 O 6158 8.00 N 5291 7.00 C 20449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 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=2.02 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 E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 91 " distance=2.03 Simple disulfide: pdb=" SG CYS F 138 " - pdb=" SG CYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 200 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 138 " - pdb=" SG CYS H 197 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 200 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 91 " distance=2.02 Simple disulfide: pdb=" SG CYS J 138 " - pdb=" SG CYS J 197 " 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: 3.11 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.7 microseconds 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7904 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 74 sheets defined 20.2% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 4.424A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 423 removed outlier: 3.814A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 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 743 Processing helix chain 'A' and resid 746 through 756 removed outlier: 4.241A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.941A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.570A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.646A pdb=" N GLY A 889 " --> 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 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.508A pdb=" N ILE A 923 " --> pdb=" O ASN A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 968 removed outlier: 5.134A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.917A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1033 Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.935A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.964A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.855A pdb=" N GLN B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 410' Processing helix chain 'B' and resid 416 through 423 removed outlier: 3.979A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 442 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.606A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.017A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 885 through 891 removed outlier: 3.556A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (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: 4.252A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.899A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.165A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.610A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.511A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.581A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.656A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.619A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 885 through 891 removed outlier: 3.889A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.855A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.854A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1035 removed outlier: 3.887A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY C1035 " --> pdb=" O GLU C1031 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.130A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.639A pdb=" N THR E 87 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 162 Processing helix chain 'F' and resid 28A through 32 Processing helix chain 'F' and resid 82 through 86 removed outlier: 4.061A pdb=" N GLU F 86 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 129 Processing helix chain 'F' and resid 185 through 192 removed outlier: 3.978A pdb=" N HIS F 192 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 65 removed outlier: 4.198A pdb=" N SER G 65 " --> pdb=" O PRO G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 82 through 86 removed outlier: 3.638A pdb=" N GLU H 86 " --> pdb=" O THR H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 removed outlier: 3.900A pdb=" N GLN H 130 " --> pdb=" O GLU H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 192 removed outlier: 3.607A pdb=" N TRP H 189 " --> pdb=" O THR H 185 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS H 190 " --> pdb=" O PRO H 186 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 65 No H-bonds generated for 'chain 'I' and resid 63 through 65' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 160 through 162 No H-bonds generated for 'chain 'I' and resid 160 through 162' Processing helix chain 'J' and resid 82 through 86 removed outlier: 3.577A pdb=" N GLU J 86 " --> pdb=" O THR J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 131 removed outlier: 3.859A pdb=" N ALA J 131 " --> pdb=" O GLU J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.807A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.503A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.115A 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: 8.229A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 225 through 229 removed outlier: 6.403A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 103 through 107 Processing sheet with id=AA7, first strand: chain 'A' and resid 314 through 318 removed outlier: 6.276A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.180A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 396 through 403 removed outlier: 3.941A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A 511 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.404A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.735A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.941A 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 1081 through 1083 removed outlier: 5.352A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.647A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY B 89 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 49 through 55 removed outlier: 4.075A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.210A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 312 removed outlier: 4.052A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 312 removed outlier: 4.052A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.591A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 541 Processing sheet with id=AC6, first strand: chain 'B' and resid 565 through 568 removed outlier: 6.780A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR B 572 " --> pdb=" O ASP B 568 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.763A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.692A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.692A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.272A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.162A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.894A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 168 through 172 removed outlier: 3.572A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 312 removed outlier: 3.679A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 312 removed outlier: 3.679A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 378 through 380 removed outlier: 4.842A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 656 removed outlier: 3.659A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.757A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE3, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AE4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE5, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.647A pdb=" N GLN E 3 " --> pdb=" O TYR E 25 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR E 21 " --> pdb=" O TRP E 7 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.861A pdb=" N ALA E 88 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER E 35 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TRP E 34 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU E 50 " --> pdb=" O TRP E 34 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN E 58 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.861A pdb=" N ALA E 88 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE E 98 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL E 102 " --> pdb=" O ILE E 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 126 through 128 removed outlier: 3.543A pdb=" N GLY E 143 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL E 146 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR E 180 " --> pdb=" O ASP E 148 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 154 through 156 removed outlier: 3.546A pdb=" N THR E 155 " --> pdb=" O ASN E 203 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR E 198 " --> pdb=" O VAL E 215 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 211 " --> pdb=" O VAL E 202 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.873A pdb=" N THR F 108 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU F 13 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 19 through 24 Processing sheet with id=AF3, first strand: chain 'F' and resid 118 through 122 removed outlier: 3.730A pdb=" N SER F 118 " --> pdb=" O SER F 141 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER F 141 " --> pdb=" O SER F 118 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA F 134 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU F 182 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR F 181 " --> pdb=" O GLU F 164 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 118 through 122 removed outlier: 3.730A pdb=" N SER F 118 " --> pdb=" O SER F 141 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER F 141 " --> pdb=" O SER F 118 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE F 143 " --> pdb=" O TYR F 176 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA F 177 " --> pdb=" O SER F 169 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER F 169 " --> pdb=" O ALA F 177 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 158 through 159 removed outlier: 4.132A pdb=" N TRP F 152 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA F 151 " --> pdb=" O GLN F 198 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN F 198 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS F 153 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER F 196 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS F 197 " --> pdb=" O LYS F 208 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS F 208 " --> pdb=" O CYS F 197 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL F 199 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL F 206 " --> pdb=" O VAL F 199 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.564A pdb=" N GLN G 3 " --> pdb=" O TYR G 25 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL G 5 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA G 23 " --> pdb=" O VAL G 5 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AF8, first strand: chain 'G' and resid 57 through 59 removed outlier: 3.716A pdb=" N ASN G 58 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TRP G 36 " --> pdb=" O GLY G 49 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN G 39 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL G 89 " --> pdb=" O GLN G 39 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 126 through 128 removed outlier: 3.756A pdb=" N LEU G 145 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY G 143 " --> pdb=" O LEU G 128 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU G 182 " --> pdb=" O VAL G 146 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 126 through 128 removed outlier: 3.756A pdb=" N LEU G 145 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY G 143 " --> pdb=" O LEU G 128 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU G 182 " --> pdb=" O VAL G 146 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER G 181 " --> pdb=" O VAL G 173 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 155 through 158 Processing sheet with id=AG3, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.722A pdb=" N THR H 6 " --> pdb=" O THR H 24 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 10 through 13 removed outlier: 4.113A pdb=" N VAL H 11 " --> pdb=" O LYS H 106 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR H 108 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU H 13 " --> pdb=" O THR H 108 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AG6, first strand: chain 'H' and resid 34 through 36 Processing sheet with id=AG7, first strand: chain 'H' and resid 134 through 143 removed outlier: 4.376A pdb=" N ALA H 134 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR H 176 " --> pdb=" O ASP H 142 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 158 through 159 removed outlier: 4.102A pdb=" N TRP H 152 " --> pdb=" O VAL H 159 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER H 196 " --> pdb=" O LYS H 153 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 158 through 159 removed outlier: 4.102A pdb=" N TRP H 152 " --> pdb=" O VAL H 159 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER H 196 " --> pdb=" O LYS H 153 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR H 195 " --> pdb=" O VAL H 210 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL H 210 " --> pdb=" O TYR H 195 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 3 through 8 removed outlier: 3.549A pdb=" N VAL I 5 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP I 7 " --> pdb=" O THR I 21 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR I 21 " --> pdb=" O TRP I 7 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU I 18 " --> pdb=" O LEU I 82 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU I 82 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 57 through 59 removed outlier: 3.601A pdb=" N ASN I 58 " --> pdb=" O LEU I 50 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TRP I 34 " --> pdb=" O LEU I 50 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN I 39 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL I 89 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS I 92 " --> pdb=" O TRP I 107 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TRP I 107 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG I 94 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU I 96 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU I 104 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE I 98 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL I 102 " --> pdb=" O ILE I 98 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 57 through 59 removed outlier: 3.601A pdb=" N ASN I 58 " --> pdb=" O LEU I 50 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TRP I 34 " --> pdb=" O LEU I 50 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN I 39 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL I 89 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR I 90 " --> pdb=" O THR I 111 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR I 111 " --> pdb=" O TYR I 90 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 124 through 128 removed outlier: 3.746A pdb=" N VAL I 185 " --> pdb=" O HIS I 168 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS I 168 " --> pdb=" O VAL I 185 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 155 through 158 Processing sheet with id=AH6, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.551A pdb=" N VAL J 19 " --> pdb=" O ILE J 78 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 10 through 13 removed outlier: 4.012A pdb=" N GLU J 13 " --> pdb=" O THR J 108 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA J 87 " --> pdb=" O LEU J 107 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 10 through 13 removed outlier: 4.012A pdb=" N GLU J 13 " --> pdb=" O THR J 108 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA J 87 " --> pdb=" O LEU J 107 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 118 through 122 removed outlier: 3.751A pdb=" N VAL J 137 " --> pdb=" O PHE J 122 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA J 134 " --> pdb=" O LEU J 184 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU J 184 " --> pdb=" O ALA J 134 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE J 140 " --> pdb=" O ALA J 178 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR J 176 " --> pdb=" O ASP J 142 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 118 through 122 removed outlier: 3.751A pdb=" N VAL J 137 " --> pdb=" O PHE J 122 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA J 134 " --> pdb=" O LEU J 184 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU J 184 " --> pdb=" O ALA J 134 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE J 140 " --> pdb=" O ALA J 178 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR J 176 " --> pdb=" O ASP J 142 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 149 through 154 removed outlier: 3.509A pdb=" N LYS J 208 " --> pdb=" O CYS J 197 " (cutoff:3.500A) 1220 hydrogen bonds defined for protein. 3234 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: 9.46 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9745 1.33 - 1.46: 7580 1.46 - 1.58: 15307 1.58 - 1.70: 0 1.70 - 1.83: 147 Bond restraints: 32779 Sorted by residual: bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.514 1.496 0.019 5.50e-03 3.31e+04 1.14e+01 bond pdb=" N VAL A 67 " pdb=" CA VAL A 67 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.19e-02 7.06e+03 9.09e+00 bond pdb=" C PHE C 855 " pdb=" N LYS C 856 " ideal model delta sigma weight residual 1.330 1.356 -0.026 1.28e-02 6.10e+03 4.24e+00 bond pdb=" N HIS A 66 " pdb=" CA HIS A 66 " ideal model delta sigma weight residual 1.462 1.488 -0.026 1.35e-02 5.49e+03 3.73e+00 bond pdb=" N ILE A 68 " pdb=" CA ILE A 68 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.57e+00 ... (remaining 32774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 44549 3.51 - 7.03: 179 7.03 - 10.54: 18 10.54 - 14.06: 1 14.06 - 17.57: 3 Bond angle restraints: 44750 Sorted by residual: angle pdb=" CB ARG A 765 " pdb=" CG ARG A 765 " pdb=" CD ARG A 765 " ideal model delta sigma weight residual 111.30 128.87 -17.57 2.30e+00 1.89e-01 5.84e+01 angle pdb=" C PHE B 559 " pdb=" N LEU B 560 " pdb=" CA LEU B 560 " ideal model delta sigma weight residual 120.68 112.28 8.40 1.52e+00 4.33e-01 3.06e+01 angle pdb=" N ARG A 765 " pdb=" CA ARG A 765 " pdb=" CB ARG A 765 " ideal model delta sigma weight residual 110.16 118.04 -7.88 1.48e+00 4.57e-01 2.84e+01 angle pdb=" C LYS A 764 " pdb=" N ARG A 765 " pdb=" CA ARG A 765 " ideal model delta sigma weight residual 120.29 112.96 7.33 1.42e+00 4.96e-01 2.66e+01 angle pdb=" CG ARG C1014 " pdb=" CD ARG C1014 " pdb=" NE ARG C1014 " ideal model delta sigma weight residual 112.00 101.27 10.73 2.20e+00 2.07e-01 2.38e+01 ... (remaining 44745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 17892 17.84 - 35.68: 1210 35.68 - 53.52: 212 53.52 - 71.36: 35 71.36 - 89.20: 21 Dihedral angle restraints: 19370 sinusoidal: 7082 harmonic: 12288 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -7.41 -78.59 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual 93.00 161.35 -68.35 1 1.00e+01 1.00e-02 6.06e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 26.30 66.70 1 1.00e+01 1.00e-02 5.80e+01 ... (remaining 19367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3924 0.051 - 0.102: 1004 0.102 - 0.153: 234 0.153 - 0.204: 16 0.204 - 0.254: 3 Chirality restraints: 5181 Sorted by residual: chirality pdb=" CB ILE C 909 " pdb=" CA ILE C 909 " pdb=" CG1 ILE C 909 " pdb=" CG2 ILE C 909 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB ILE B 664 " pdb=" CA ILE B 664 " pdb=" CG1 ILE B 664 " pdb=" CG2 ILE B 664 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE C 726 " pdb=" CA ILE C 726 " pdb=" CG1 ILE C 726 " pdb=" CG2 ILE C 726 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 5178 not shown) Planarity restraints: 5746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.078 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO C 986 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 144 " 0.068 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO H 145 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO H 145 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO H 145 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C1014 " 0.298 9.50e-02 1.11e+02 1.34e-01 1.30e+01 pdb=" NE ARG C1014 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG C1014 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG C1014 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C1014 " 0.003 2.00e-02 2.50e+03 ... (remaining 5743 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 216 2.44 - 3.06: 21489 3.06 - 3.67: 49462 3.67 - 4.29: 69212 4.29 - 4.90: 112833 Nonbonded interactions: 253212 Sorted by model distance: nonbonded pdb=" O LEU A 977 " pdb=" CD2 PHE A 981 " model vdw 1.825 3.340 nonbonded pdb=" O ASP A 290 " pdb=" OG SER A 297 " model vdw 1.981 3.040 nonbonded pdb=" O LEU A 387 " pdb=" CB SER A 530 " model vdw 1.984 3.440 nonbonded pdb=" O GLU C 309 " pdb=" OH TYR C 313 " model vdw 2.083 3.040 nonbonded pdb=" CG1 ILE C 95 " pdb=" CD1 LEU C 189 " model vdw 2.093 3.860 ... (remaining 253207 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 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 51 or (res \ id 52 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 86 or (resid 87 and (name N or name CA or name C or name O or name \ CB )) or resid 88 through 96 or (resid 97 through 98 and (name N or name CA or \ name C or name O or name CB )) or resid 99 through 114 or (resid 115 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 133 or (resid \ 134 and (name N or name CA or name C or name O or name CB )) or resid 135 throu \ gh 136 or (resid 137 and (name N or name CA or name C or name O or name CB )) or \ resid 138 through 318 or (resid 319 and (name N or name CA or name C or name O \ or name CB )) or resid 320 through 329 or resid 337 through 455 or resid 462 thr \ ough 469 or resid 492 through 518 or resid 531 through 553 or (resid 554 and (na \ me N or name CA or name C or name O or name CB )) or resid 555 or (resid 556 thr \ ough 558 and (name N or name CA or name C or name O or name CB )) or resid 559 t \ hrough 563 or (resid 564 and (name N or name CA or name C or name O or name CB ) \ ) or resid 565 through 570 or (resid 571 through 572 and (name N or name CA or n \ ame C or name O or name CB )) or resid 573 through 591 or (resid 592 and (name N \ or name CA or name C or name O or name CB )) or resid 593 through 620 or resid \ 641 through 676 or (resid 690 and (name N or name CA or name C or name O or name \ CB )) or resid 691 through 747 or (resid 748 and (name N or name CA or name C o \ r name O or name CB )) or resid 749 through 827 or (resid 828 and (name N or nam \ e CA or name C or name O or name CB )) or resid 855 through 984 or (resid 985 an \ d (name N or name CA or name C or name O or name CB )) or resid 986 through 987 \ or (resid 988 through 989 and (name N or name CA or name C or name O or name CB \ )) or resid 990 through 993 or (resid 994 and (name N or name CA or name C or na \ me O or name CB )) or resid 995 through 1037 or (resid 1038 and (name N or name \ CA or name C or name O or name CB )) or resid 1039 through 1050 or (resid 1051 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1052 through 11 \ 10 or (resid 1111 and (name N or name CA or name C or name O or name CB )) or re \ sid 1112 through 1143 or (resid 1144 through 1146 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'B' and (resid 27 through 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 51 or (res \ id 52 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 68 or resid 82 through 86 or (resid 87 and (name N or name CA or n \ ame C or name O or name CB )) or resid 88 through 96 or (resid 97 through 98 and \ (name N or name CA or name C or name O or name CB )) or resid 99 through 114 or \ (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 6 through 133 or (resid 134 and (name N or name CA or name C or name O or name C \ B )) or resid 135 through 136 or (resid 137 and (name N or name CA or name C or \ name O or name CB )) or resid 138 through 248 or resid 256 through 318 or (resid \ 319 and (name N or name CA or name C or name O or name CB )) or resid 320 throu \ gh 329 or resid 337 through 455 or resid 462 through 469 or resid 492 through 51 \ 8 or resid 523 or resid 532 through 553 or (resid 554 and (name N or name CA or \ name C or name O or name CB )) or resid 555 or (resid 556 through 558 and (name \ N or name CA or name C or name O or name CB )) or resid 559 through 563 or (resi \ d 564 and (name N or name CA or name C or name O or name CB )) or resid 565 thro \ ugh 570 or (resid 571 through 572 and (name N or name CA or name C or name O or \ name CB )) or resid 573 through 591 or (resid 592 and (name N or name CA or name \ C or name O or name CB )) or resid 593 through 620 or resid 641 through 676 or \ (resid 690 and (name N or name CA or name C or name O or name CB )) or resid 691 \ through 747 or (resid 748 and (name N or name CA or name C or name O or name CB \ )) or resid 749 through 827 or (resid 828 and (name N or name CA or name C or n \ ame O or name CB )) or resid 855 through 984 or (resid 985 and (name N or name C \ A or name C or name O or name CB )) or resid 986 through 987 or (resid 988 throu \ gh 989 and (name N or name CA or name C or name O or name CB )) or resid 990 thr \ ough 1037 or (resid 1038 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1039 through 1050 or (resid 1051 and (name N or name CA or name C or \ name O or name CB )) or resid 1052 through 1110 or (resid 1111 and (name N or na \ me CA or name C or name O or name CB )) or resid 1112 through 1143 or (resid 114 \ 4 through 1146 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 67 or (resid 68 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 107 or (resid 108 thr \ ough 113 and (name N or name CA or name C or name O or name CB )) or resid 114 t \ hrough 175 or (resid 176 through 187 and (name N or name CA or name C or name O \ or name CB )) or resid 188 through 199 or (resid 200 and (name N or name CA or n \ ame C or name O or name CB )) or resid 201 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 223 or (resid \ 224 and (name N or name CA or name C or name O or name CB )) or resid 225 throu \ gh 248 or resid 256 through 303 or (resid 304 and (name N or name CA or name C o \ r name O or name CB )) or resid 305 through 320 or (resid 321 and (name N or nam \ e CA or name C or name O or name CB )) or resid 322 through 329 or resid 337 thr \ ough 469 or resid 492 through 518 or resid 523 or resid 532 through 546 or (resi \ d 547 and (name N or name CA or name C or name O or name CB )) or resid 548 thro \ ugh 556 or (resid 557 through 558 and (name N or name CA or name C or name O or \ name CB )) or resid 559 through 568 or (resid 569 through 572 and (name N or nam \ e CA or name C or name O or name CB )) or resid 573 through 662 or (resid 663 an \ d (name N or name CA or name C or name O or name CB )) or resid 664 through 701 \ or (resid 702 and (name N or name CA or name C or name O or name CB )) or resid \ 703 through 739 or (resid 740 and (name N or name CA or name C or name O or name \ CB )) or resid 741 through 794 or (resid 795 and (name N or name CA or name C o \ r name O or name CB )) or resid 796 through 807 or (resid 808 and (name N or nam \ e CA or name C or name O or name CB )) or resid 809 through 818 or (resid 819 an \ d (name N or name CA or name C or name O or name CB )) or resid 820 through 824 \ or (resid 825 and (name N or name CA or name C or name O or name CB )) or resid \ 826 through 855 or (resid 856 and (name N or name CA or name C or name O or name \ CB )) or resid 857 through 917 or (resid 918 and (name N or name CA or name C o \ r name O or name CB )) or resid 919 through 946 or (resid 947 and (name N or nam \ e CA or name C or name O or name CB )) or resid 948 through 963 or (resid 964 an \ d (name N or name CA or name C or name O or name CB )) or resid 965 through 993 \ or (resid 994 and (name N or name CA or name C or name O or name CB )) or resid \ 995 through 1072 or (resid 1073 and (name N or name CA or name C or name O or na \ me CB )) or resid 1074 through 1137 or (resid 1138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1139 through 1140 or (resid 1141 through 11 \ 42 and (name N or name CA or name C or name O or name CB )) or resid 1143 throug \ h 1145 or (resid 1146 and (name N or name CA or name C or name O or name CB )))) \ } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.050 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 35.560 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5058 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 : 0.004 0.104 32825 Z= 0.210 Angle : 0.737 17.575 44842 Z= 0.406 Chirality : 0.048 0.254 5181 Planarity : 0.006 0.134 5746 Dihedral : 12.440 89.201 11328 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.56 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -1.30 (0.13), residues: 4159 helix: -0.79 (0.19), residues: 638 sheet: -0.06 (0.16), residues: 1054 loop : -1.26 (0.12), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG C1014 TYR 0.036 0.002 TYR F 50 PHE 0.027 0.002 PHE C 906 TRP 0.026 0.002 TRP E 34 HIS 0.031 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00426 (32779) covalent geometry : angle 0.73535 (44750) SS BOND : bond 0.00425 ( 46) SS BOND : angle 1.25473 ( 92) hydrogen bonds : bond 0.22214 ( 1165) hydrogen bonds : angle 9.20128 ( 3234) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 953 ASN cc_start: 0.7706 (m110) cc_final: 0.7161 (m110) REVERT: B 997 ILE cc_start: 0.7308 (mm) cc_final: 0.5948 (mm) REVERT: C 95 ILE cc_start: 0.4114 (mt) cc_final: 0.3898 (mp) REVERT: C 773 GLU cc_start: 0.6517 (tt0) cc_final: 0.6303 (mt-10) REVERT: F 11 VAL cc_start: 0.6314 (t) cc_final: 0.5805 (p) outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 0.1927 time to fit residues: 128.9818 Evaluate side-chains 330 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 762 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 955 ASN B 965 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 960 ASN C1010 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5140 r_free = 0.5140 target = 0.249216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.225853 restraints weight = 106765.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.222655 restraints weight = 127514.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.222044 restraints weight = 135905.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.220912 restraints weight = 114478.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.221061 restraints weight = 111420.100| |-----------------------------------------------------------------------------| r_work (final): 0.4813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5261 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 32825 Z= 0.151 Angle : 0.619 8.642 44842 Z= 0.333 Chirality : 0.046 0.170 5181 Planarity : 0.005 0.073 5746 Dihedral : 5.077 23.178 4492 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.22 % Favored : 94.76 % Rotamer: Outliers : 0.14 % Allowed : 4.75 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -1.06 (0.13), residues: 4159 helix: -0.22 (0.19), residues: 664 sheet: -0.01 (0.16), residues: 1128 loop : -1.20 (0.13), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1014 TYR 0.024 0.002 TYR F 50 PHE 0.038 0.002 PHE B 981 TRP 0.018 0.001 TRP E 34 HIS 0.015 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00314 (32779) covalent geometry : angle 0.61742 (44750) SS BOND : bond 0.00360 ( 46) SS BOND : angle 1.23865 ( 92) hydrogen bonds : bond 0.05040 ( 1165) hydrogen bonds : angle 7.12472 ( 3234) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 396 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.6411 (m-80) cc_final: 0.5916 (m-10) REVERT: B 239 GLN cc_start: 0.5021 (mp10) cc_final: 0.4726 (mm-40) REVERT: B 565 PHE cc_start: 0.7463 (p90) cc_final: 0.7174 (p90) REVERT: B 1006 THR cc_start: 0.8783 (m) cc_final: 0.8548 (m) REVERT: B 1028 LYS cc_start: 0.8393 (mttm) cc_final: 0.8054 (mmtp) REVERT: C 773 GLU cc_start: 0.7437 (tt0) cc_final: 0.6957 (mt-10) REVERT: I 96 LEU cc_start: 0.5766 (pp) cc_final: 0.5517 (mm) outliers start: 5 outliers final: 1 residues processed: 401 average time/residue: 0.1939 time to fit residues: 127.6763 Evaluate side-chains 324 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 239 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 381 optimal weight: 20.0000 chunk 111 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 259 optimal weight: 8.9990 chunk 233 optimal weight: 0.8980 chunk 30 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN B 196 ASN B 955 ASN B 965 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 784 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN J 35 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5158 r_free = 0.5158 target = 0.251704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.229155 restraints weight = 106618.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.226807 restraints weight = 140363.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.224438 restraints weight = 124895.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.223428 restraints weight = 127819.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.223395 restraints weight = 110486.799| |-----------------------------------------------------------------------------| r_work (final): 0.4832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5215 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32825 Z= 0.120 Angle : 0.579 10.494 44842 Z= 0.308 Chirality : 0.045 0.171 5181 Planarity : 0.005 0.067 5746 Dihedral : 4.817 21.834 4492 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.91 % Favored : 95.07 % Rotamer: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -0.95 (0.13), residues: 4159 helix: -0.15 (0.19), residues: 670 sheet: 0.03 (0.16), residues: 1133 loop : -1.11 (0.13), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 765 TYR 0.035 0.001 TYR F 50 PHE 0.024 0.001 PHE B 981 TRP 0.020 0.001 TRP E 34 HIS 0.010 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00263 (32779) covalent geometry : angle 0.57725 (44750) SS BOND : bond 0.00325 ( 46) SS BOND : angle 1.06446 ( 92) hydrogen bonds : bond 0.04266 ( 1165) hydrogen bonds : angle 6.61205 ( 3234) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 416 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.6279 (m-80) cc_final: 0.5803 (m-10) REVERT: A 914 ASN cc_start: 0.8043 (t0) cc_final: 0.7435 (t0) REVERT: B 565 PHE cc_start: 0.7535 (p90) cc_final: 0.7230 (p90) REVERT: B 900 MET cc_start: 0.3711 (mpp) cc_final: 0.2743 (mpp) REVERT: B 1028 LYS cc_start: 0.8433 (mttm) cc_final: 0.8064 (mmtp) REVERT: C 773 GLU cc_start: 0.7330 (tt0) cc_final: 0.6803 (mt-10) REVERT: C 1012 LEU cc_start: 0.9137 (mt) cc_final: 0.8936 (mt) REVERT: G 29 PHE cc_start: 0.2590 (m-80) cc_final: 0.2373 (m-80) outliers start: 3 outliers final: 0 residues processed: 419 average time/residue: 0.1807 time to fit residues: 124.8483 Evaluate side-chains 329 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 233 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 97 optimal weight: 30.0000 chunk 349 optimal weight: 40.0000 chunk 81 optimal weight: 0.2980 chunk 420 optimal weight: 6.9990 chunk 361 optimal weight: 40.0000 chunk 27 optimal weight: 8.9990 chunk 123 optimal weight: 0.0870 chunk 239 optimal weight: 9.9990 chunk 385 optimal weight: 10.0000 overall best weight: 1.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 196 ASN B 965 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 HIS G 76 ASN H 35 GLN ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5151 r_free = 0.5151 target = 0.250578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.227818 restraints weight = 106031.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.225243 restraints weight = 155150.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.223281 restraints weight = 133518.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.222414 restraints weight = 130264.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.222974 restraints weight = 105292.066| |-----------------------------------------------------------------------------| r_work (final): 0.4739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5343 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32825 Z= 0.133 Angle : 0.582 10.031 44842 Z= 0.308 Chirality : 0.045 0.202 5181 Planarity : 0.005 0.063 5746 Dihedral : 4.766 22.294 4492 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.34 % Favored : 94.64 % Rotamer: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -0.93 (0.13), residues: 4159 helix: -0.03 (0.20), residues: 658 sheet: 0.01 (0.16), residues: 1136 loop : -1.10 (0.13), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1019 TYR 0.024 0.001 TYR C 351 PHE 0.020 0.001 PHE B 981 TRP 0.014 0.001 TRP A 886 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00290 (32779) covalent geometry : angle 0.58022 (44750) SS BOND : bond 0.00274 ( 46) SS BOND : angle 1.13846 ( 92) hydrogen bonds : bond 0.04095 ( 1165) hydrogen bonds : angle 6.44546 ( 3234) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 398 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.6078 (m-80) cc_final: 0.5541 (m-10) REVERT: A 914 ASN cc_start: 0.8127 (t0) cc_final: 0.7538 (t0) REVERT: B 41 LYS cc_start: 0.3701 (mmtt) cc_final: 0.2622 (tptt) REVERT: B 565 PHE cc_start: 0.8014 (p90) cc_final: 0.7485 (p90) REVERT: B 723 THR cc_start: 0.8094 (m) cc_final: 0.7759 (p) REVERT: B 900 MET cc_start: 0.3782 (mpp) cc_final: 0.2627 (tpp) REVERT: B 965 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7271 (tp40) REVERT: B 997 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8171 (mm) REVERT: C 733 LYS cc_start: 0.7861 (pttm) cc_final: 0.7516 (pttm) REVERT: C 773 GLU cc_start: 0.8187 (tt0) cc_final: 0.7647 (mt-10) REVERT: C 775 ASP cc_start: 0.7717 (m-30) cc_final: 0.7453 (m-30) REVERT: E 149 TYR cc_start: 0.3114 (p90) cc_final: 0.2909 (p90) REVERT: F 92 GLN cc_start: 0.6310 (tp40) cc_final: 0.5695 (tp40) REVERT: G 29 PHE cc_start: 0.1909 (m-80) cc_final: 0.1612 (m-80) REVERT: I 58 ASN cc_start: 0.7048 (m-40) cc_final: 0.6688 (m110) REVERT: I 109 GLN cc_start: 0.7465 (tm-30) cc_final: 0.6464 (pm20) outliers start: 2 outliers final: 0 residues processed: 399 average time/residue: 0.1826 time to fit residues: 119.8290 Evaluate side-chains 336 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 334 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 210 optimal weight: 20.0000 chunk 208 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 328 optimal weight: 7.9990 chunk 162 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 255 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN B 196 ASN B 239 GLN B 955 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5126 r_free = 0.5126 target = 0.247703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.224233 restraints weight = 106727.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.218805 restraints weight = 143493.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.216967 restraints weight = 136032.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.215340 restraints weight = 124591.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.215664 restraints weight = 117712.737| |-----------------------------------------------------------------------------| r_work (final): 0.4777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5430 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 32825 Z= 0.169 Angle : 0.619 9.868 44842 Z= 0.327 Chirality : 0.047 0.293 5181 Planarity : 0.005 0.070 5746 Dihedral : 4.901 21.735 4492 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.94 % Favored : 94.04 % Rotamer: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -1.02 (0.13), residues: 4159 helix: -0.16 (0.19), residues: 659 sheet: 0.03 (0.16), residues: 1097 loop : -1.17 (0.13), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 567 TYR 0.020 0.002 TYR A 873 PHE 0.020 0.002 PHE C 718 TRP 0.013 0.001 TRP E 34 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00366 (32779) covalent geometry : angle 0.61772 (44750) SS BOND : bond 0.00367 ( 46) SS BOND : angle 1.18303 ( 92) hydrogen bonds : bond 0.04370 ( 1165) hydrogen bonds : angle 6.51665 ( 3234) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 399 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7261 (mtm-85) cc_final: 0.7055 (mtm-85) REVERT: A 306 PHE cc_start: 0.6578 (m-80) cc_final: 0.5916 (m-10) REVERT: A 733 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7537 (mtpt) REVERT: B 565 PHE cc_start: 0.7530 (p90) cc_final: 0.7221 (p90) REVERT: B 900 MET cc_start: 0.3791 (mpp) cc_final: 0.3016 (mpp) REVERT: B 1006 THR cc_start: 0.8465 (m) cc_final: 0.7977 (m) REVERT: C 773 GLU cc_start: 0.8041 (tt0) cc_final: 0.7782 (mt-10) REVERT: G 29 PHE cc_start: 0.2444 (m-80) cc_final: 0.1953 (m-80) outliers start: 2 outliers final: 0 residues processed: 400 average time/residue: 0.1917 time to fit residues: 127.2883 Evaluate side-chains 336 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 214 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 339 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 371 optimal weight: 8.9990 chunk 390 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5133 r_free = 0.5133 target = 0.248422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.224816 restraints weight = 105965.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.221645 restraints weight = 114808.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.221524 restraints weight = 126803.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.219899 restraints weight = 106450.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.220343 restraints weight = 102617.129| |-----------------------------------------------------------------------------| r_work (final): 0.4804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5293 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 32825 Z= 0.148 Angle : 0.604 10.289 44842 Z= 0.318 Chirality : 0.046 0.334 5181 Planarity : 0.005 0.063 5746 Dihedral : 4.860 21.593 4492 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.58 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -1.02 (0.13), residues: 4159 helix: -0.11 (0.20), residues: 661 sheet: 0.03 (0.16), residues: 1086 loop : -1.19 (0.13), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1019 TYR 0.023 0.001 TYR C 265 PHE 0.022 0.002 PHE B 92 TRP 0.018 0.001 TRP E 34 HIS 0.009 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00323 (32779) covalent geometry : angle 0.60217 (44750) SS BOND : bond 0.00332 ( 46) SS BOND : angle 1.13405 ( 92) hydrogen bonds : bond 0.04136 ( 1165) hydrogen bonds : angle 6.40766 ( 3234) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.6418 (m-80) cc_final: 0.5840 (m-10) REVERT: B 41 LYS cc_start: 0.3695 (mmtt) cc_final: 0.2600 (ptpp) REVERT: B 565 PHE cc_start: 0.7764 (p90) cc_final: 0.7413 (p90) REVERT: B 900 MET cc_start: 0.3735 (mpp) cc_final: 0.2942 (mpp) REVERT: B 1075 PHE cc_start: 0.5235 (m-80) cc_final: 0.5006 (m-80) REVERT: C 773 GLU cc_start: 0.7427 (tt0) cc_final: 0.7007 (tt0) REVERT: F 92 GLN cc_start: 0.5130 (tp40) cc_final: 0.4759 (tp40) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.1999 time to fit residues: 134.8395 Evaluate side-chains 345 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 319 optimal weight: 0.9980 chunk 113 optimal weight: 20.0000 chunk 314 optimal weight: 7.9990 chunk 409 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 270 optimal weight: 1.9990 chunk 316 optimal weight: 5.9990 chunk 234 optimal weight: 0.5980 chunk 259 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN B 196 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5147 r_free = 0.5147 target = 0.250108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.228030 restraints weight = 106117.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.225924 restraints weight = 134018.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.224147 restraints weight = 130651.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.223300 restraints weight = 115906.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.223424 restraints weight = 104783.377| |-----------------------------------------------------------------------------| r_work (final): 0.4754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32825 Z= 0.122 Angle : 0.588 9.817 44842 Z= 0.309 Chirality : 0.046 0.205 5181 Planarity : 0.005 0.061 5746 Dihedral : 4.742 22.019 4492 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.12 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -0.95 (0.13), residues: 4159 helix: -0.03 (0.20), residues: 656 sheet: 0.14 (0.16), residues: 1084 loop : -1.18 (0.13), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1014 TYR 0.026 0.001 TYR H 37 PHE 0.020 0.001 PHE B 927 TRP 0.019 0.001 TRP B 104 HIS 0.025 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00269 (32779) covalent geometry : angle 0.58629 (44750) SS BOND : bond 0.00255 ( 46) SS BOND : angle 1.20894 ( 92) hydrogen bonds : bond 0.03883 ( 1165) hydrogen bonds : angle 6.26321 ( 3234) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.5988 (m-80) cc_final: 0.5459 (m-10) REVERT: A 316 SER cc_start: 0.6784 (p) cc_final: 0.6484 (p) REVERT: A 727 LEU cc_start: 0.8533 (mt) cc_final: 0.8321 (mt) REVERT: A 820 ASP cc_start: 0.8472 (m-30) cc_final: 0.8238 (m-30) REVERT: A 902 MET cc_start: 0.6085 (tmm) cc_final: 0.5756 (tmm) REVERT: A 914 ASN cc_start: 0.8165 (t160) cc_final: 0.7624 (t0) REVERT: B 565 PHE cc_start: 0.8039 (p90) cc_final: 0.7464 (p90) REVERT: B 900 MET cc_start: 0.3824 (mpp) cc_final: 0.3072 (mpp) REVERT: B 1000 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7948 (mmm-85) REVERT: B 1075 PHE cc_start: 0.6089 (m-80) cc_final: 0.5680 (m-80) REVERT: B 1109 PHE cc_start: 0.6599 (t80) cc_final: 0.6322 (t80) REVERT: C 996 LEU cc_start: 0.8693 (mt) cc_final: 0.8406 (mt) REVERT: C 1023 ASN cc_start: 0.8168 (m110) cc_final: 0.7951 (m110) REVERT: E 149 TYR cc_start: 0.3419 (p90) cc_final: 0.3136 (p90) REVERT: F 4 MET cc_start: -0.1889 (tpp) cc_final: -0.2266 (tpp) REVERT: F 89 TYR cc_start: 0.4356 (m-80) cc_final: 0.3908 (m-80) REVERT: F 92 GLN cc_start: 0.5730 (tp40) cc_final: 0.5117 (tp40) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.1998 time to fit residues: 133.8466 Evaluate side-chains 348 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 43 optimal weight: 10.0000 chunk 228 optimal weight: 9.9990 chunk 217 optimal weight: 5.9990 chunk 410 optimal weight: 9.9990 chunk 353 optimal weight: 4.9990 chunk 389 optimal weight: 0.0980 chunk 79 optimal weight: 0.0970 chunk 88 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 234 optimal weight: 20.0000 chunk 127 optimal weight: 0.0040 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 751 ASN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5151 r_free = 0.5151 target = 0.250512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.228148 restraints weight = 106280.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.224683 restraints weight = 136325.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.223037 restraints weight = 138984.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.222318 restraints weight = 123476.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.221904 restraints weight = 113484.229| |-----------------------------------------------------------------------------| r_work (final): 0.4822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5236 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32825 Z= 0.120 Angle : 0.586 9.995 44842 Z= 0.307 Chirality : 0.046 0.204 5181 Planarity : 0.005 0.075 5746 Dihedral : 4.677 24.450 4492 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.03 % Favored : 94.95 % Rotamer: Outliers : 0.03 % Allowed : 0.98 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -0.88 (0.13), residues: 4159 helix: 0.05 (0.20), residues: 650 sheet: 0.18 (0.16), residues: 1086 loop : -1.14 (0.13), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1019 TYR 0.024 0.001 TYR A 873 PHE 0.017 0.001 PHE I 99 TRP 0.014 0.001 TRP E 34 HIS 0.018 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00268 (32779) covalent geometry : angle 0.58346 (44750) SS BOND : bond 0.00265 ( 46) SS BOND : angle 1.22945 ( 92) hydrogen bonds : bond 0.03763 ( 1165) hydrogen bonds : angle 6.17148 ( 3234) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 413 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7396 (mp) cc_final: 0.7124 (mp) REVERT: A 306 PHE cc_start: 0.6362 (m-80) cc_final: 0.5611 (m-10) REVERT: A 316 SER cc_start: 0.6119 (p) cc_final: 0.5804 (p) REVERT: A 914 ASN cc_start: 0.8212 (t0) cc_final: 0.7941 (t0) REVERT: B 41 LYS cc_start: 0.3565 (mptt) cc_final: 0.2654 (tptt) REVERT: B 565 PHE cc_start: 0.7676 (p90) cc_final: 0.7301 (p90) REVERT: B 900 MET cc_start: 0.3490 (mpp) cc_final: 0.2845 (mpp) REVERT: B 995 ARG cc_start: 0.7202 (ptp90) cc_final: 0.6876 (ptp90) REVERT: C 1012 LEU cc_start: 0.9220 (mt) cc_final: 0.9019 (mt) REVERT: E 53 HIS cc_start: 0.6083 (t70) cc_final: 0.5879 (p-80) REVERT: F 4 MET cc_start: -0.1633 (tpp) cc_final: -0.1938 (tpp) REVERT: F 92 GLN cc_start: 0.5465 (tp40) cc_final: 0.5058 (tp40) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.2019 time to fit residues: 137.8454 Evaluate side-chains 339 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 232 optimal weight: 30.0000 chunk 166 optimal weight: 0.0980 chunk 402 optimal weight: 5.9990 chunk 308 optimal weight: 6.9990 chunk 115 optimal weight: 30.0000 chunk 250 optimal weight: 6.9990 chunk 334 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 344 optimal weight: 50.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1054 GLN B 196 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5105 r_free = 0.5105 target = 0.245257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.221730 restraints weight = 105791.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.216143 restraints weight = 119778.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.211770 restraints weight = 122967.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.211036 restraints weight = 125705.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.211319 restraints weight = 111693.981| |-----------------------------------------------------------------------------| r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5656 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 32825 Z= 0.210 Angle : 0.689 9.678 44842 Z= 0.363 Chirality : 0.049 0.389 5181 Planarity : 0.006 0.115 5746 Dihedral : 5.108 25.468 4492 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.80 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -1.19 (0.13), residues: 4159 helix: -0.47 (0.19), residues: 660 sheet: 0.01 (0.16), residues: 1074 loop : -1.27 (0.12), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 995 TYR 0.025 0.002 TYR A 741 PHE 0.022 0.002 PHE C 718 TRP 0.022 0.002 TRP C 886 HIS 0.020 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00455 (32779) covalent geometry : angle 0.68628 (44750) SS BOND : bond 0.00659 ( 46) SS BOND : angle 1.42777 ( 92) hydrogen bonds : bond 0.04535 ( 1165) hydrogen bonds : angle 6.60315 ( 3234) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.6043 (m-80) cc_final: 0.5409 (m-10) REVERT: A 567 ARG cc_start: 0.8197 (tpp80) cc_final: 0.7860 (tpp80) REVERT: A 727 LEU cc_start: 0.8379 (mt) cc_final: 0.8147 (mt) REVERT: A 733 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7858 (mtpt) REVERT: A 1009 THR cc_start: 0.9016 (m) cc_final: 0.8816 (m) REVERT: B 565 PHE cc_start: 0.8173 (p90) cc_final: 0.7499 (p90) REVERT: B 900 MET cc_start: 0.3915 (mpp) cc_final: 0.3543 (mpp) REVERT: B 995 ARG cc_start: 0.7906 (ptp90) cc_final: 0.7591 (ptp90) REVERT: B 1109 PHE cc_start: 0.6902 (t80) cc_final: 0.6553 (t80) REVERT: C 772 VAL cc_start: 0.8918 (t) cc_final: 0.8652 (t) REVERT: C 950 ASP cc_start: 0.8389 (m-30) cc_final: 0.8072 (m-30) REVERT: C 1023 ASN cc_start: 0.8402 (m110) cc_final: 0.8165 (m110) REVERT: E 53 HIS cc_start: 0.6733 (t70) cc_final: 0.6162 (p-80) REVERT: E 149 TYR cc_start: 0.3159 (p90) cc_final: 0.2895 (p90) REVERT: F 4 MET cc_start: -0.2146 (tpp) cc_final: -0.2481 (tpp) REVERT: F 92 GLN cc_start: 0.5906 (tp40) cc_final: 0.5457 (tp40) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.1994 time to fit residues: 128.3859 Evaluate side-chains 327 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 255 optimal weight: 0.9980 chunk 329 optimal weight: 30.0000 chunk 376 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 311 optimal weight: 20.0000 chunk 44 optimal weight: 0.4980 chunk 249 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN A 935 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 955 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.246491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.223138 restraints weight = 106124.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.219376 restraints weight = 118636.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.220115 restraints weight = 128274.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.218983 restraints weight = 100351.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.218826 restraints weight = 108337.890| |-----------------------------------------------------------------------------| r_work (final): 0.4818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5312 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 32825 Z= 0.168 Angle : 0.646 10.146 44842 Z= 0.339 Chirality : 0.048 0.312 5181 Planarity : 0.005 0.068 5746 Dihedral : 5.076 24.281 4492 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.16 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -1.21 (0.13), residues: 4159 helix: -0.43 (0.19), residues: 653 sheet: -0.04 (0.16), residues: 1066 loop : -1.28 (0.12), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1091 TYR 0.042 0.002 TYR J 90 PHE 0.021 0.002 PHE C 718 TRP 0.017 0.001 TRP E 34 HIS 0.019 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00368 (32779) covalent geometry : angle 0.64342 (44750) SS BOND : bond 0.00353 ( 46) SS BOND : angle 1.35974 ( 92) hydrogen bonds : bond 0.04316 ( 1165) hydrogen bonds : angle 6.48326 ( 3234) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.6353 (m-80) cc_final: 0.5615 (m-10) REVERT: A 733 LYS cc_start: 0.8010 (mtpt) cc_final: 0.7617 (mtpt) REVERT: A 1064 HIS cc_start: 0.6325 (m-70) cc_final: 0.5707 (m-70) REVERT: A 1139 ASP cc_start: 0.6623 (t0) cc_final: 0.6103 (m-30) REVERT: B 565 PHE cc_start: 0.7751 (p90) cc_final: 0.7367 (p90) REVERT: C 773 GLU cc_start: 0.7994 (tt0) cc_final: 0.7524 (tt0) REVERT: F 4 MET cc_start: -0.1454 (tpp) cc_final: -0.1829 (tpp) REVERT: G 29 PHE cc_start: 0.2875 (m-80) cc_final: 0.2595 (m-80) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.1942 time to fit residues: 125.0590 Evaluate side-chains 324 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 348 optimal weight: 20.0000 chunk 289 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 309 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 407 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 955 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 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 = 0.5120 r_free = 0.5120 target = 0.246979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.223759 restraints weight = 106059.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.220893 restraints weight = 153697.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.221046 restraints weight = 152391.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.220109 restraints weight = 116717.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.220239 restraints weight = 114202.677| |-----------------------------------------------------------------------------| r_work (final): 0.4836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5268 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 32825 Z= 0.153 Angle : 0.634 9.928 44842 Z= 0.333 Chirality : 0.047 0.279 5181 Planarity : 0.005 0.066 5746 Dihedral : 5.024 23.519 4492 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.42 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -1.19 (0.13), residues: 4159 helix: -0.40 (0.19), residues: 653 sheet: -0.05 (0.16), residues: 1066 loop : -1.26 (0.12), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C1014 TYR 0.022 0.001 TYR H 37 PHE 0.037 0.002 PHE C 797 TRP 0.016 0.001 TRP E 34 HIS 0.019 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00337 (32779) covalent geometry : angle 0.63175 (44750) SS BOND : bond 0.00285 ( 46) SS BOND : angle 1.30520 ( 92) hydrogen bonds : bond 0.04175 ( 1165) hydrogen bonds : angle 6.43311 ( 3234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5684.89 seconds wall clock time: 99 minutes 26.36 seconds (5966.36 seconds total)