Starting phenix.real_space_refine on Tue Aug 26 17:38:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsl_38621/08_2025/8xsl_38621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsl_38621/08_2025/8xsl_38621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xsl_38621/08_2025/8xsl_38621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsl_38621/08_2025/8xsl_38621.map" model { file = "/net/cci-nas-00/data/ceres_data/8xsl_38621/08_2025/8xsl_38621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsl_38621/08_2025/8xsl_38621.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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 11087 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 129 5.16 5 C 19238 2.51 5 N 5026 2.21 5 O 5874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s 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: 30267 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7817 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1001, 7811 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 49, 'TRANS': 951} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1001, 7811 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 49, 'TRANS': 951} Chain breaks: 8 bond proxies already assigned to first conformer: 7978 Chain: "B" Number of atoms: 7817 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1001, 7811 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 49, 'TRANS': 951} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1001, 7811 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 49, 'TRANS': 951} Chain breaks: 8 bond proxies already assigned to first conformer: 7978 Chain: "C" Number of atoms: 7829 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 bond proxies already assigned to first conformer: 7992 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1658 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 210} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1611 Classifications: {'peptide': 212} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 201} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "M" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1658 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 210} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1611 Classifications: {'peptide': 212} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 201} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 11.43, per 1000 atoms: 0.38 Number of scatterers: 30267 At special positions: 0 Unit cell: (143.65, 226.95, 208.25, 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 129 16.00 O 5874 8.00 N 5026 7.00 C 19238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, 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 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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=2.03 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=2.03 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 480 " - pdb=" SG CYS B 488 " 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 150 " - pdb=" SG CYS M 206 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A1134 " " NAG A1305 " - " ASN A 61 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 717 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B1098 " " NAG B1306 " - " ASN B1134 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C 717 " " NAG C1304 " - " ASN C1134 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 717 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7228 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 67 sheets defined 21.4% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.909A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.259A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.606A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.603A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.547A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.033A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.079A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.777A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.271A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.333A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.851A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.932A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.637A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.509A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.123A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.122A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.662A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.788A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.281A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.769A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.710A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.602A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.503A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.136A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.149A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.502A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.721A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) 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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.622A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.383A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.573A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 168 removed outlier: 3.739A pdb=" N ALA H 168 " --> pdb=" O TRP H 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.537A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.991A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.825A pdb=" N THR M 91 " --> pdb=" O ALA M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 168 removed outlier: 3.747A pdb=" N ALA M 168 " --> pdb=" O TRP M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 199 No H-bonds generated for 'chain 'M' and resid 197 through 199' Processing helix chain 'N' and resid 121 through 126 removed outlier: 3.704A pdb=" N LYS N 126 " --> pdb=" O ASP N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 189 removed outlier: 3.754A pdb=" N HIS N 189 " --> pdb=" O ASP N 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.591A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.969A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.998A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.210A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.626A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.277A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.923A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.514A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.875A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.464A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.464A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.562A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.841A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.418A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.111A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.842A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.643A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.044A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.060A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.475A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.475A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD6, first strand: chain 'B' and resid 1086 through 1090 removed outlier: 4.538A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.432A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.108A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.895A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.877A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.658A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.515A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.986A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.524A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.524A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF3, first strand: chain 'C' and resid 1086 through 1090 removed outlier: 4.615A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.971A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF7, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.111A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.111A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 161 through 162 Processing sheet with id=AG1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.853A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.542A pdb=" N VAL L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.062A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 146 through 150 Processing sheet with id=AG5, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AG6, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.788A pdb=" N MET M 34 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AG8, first strand: chain 'M' and resid 130 through 134 removed outlier: 6.452A pdb=" N SER M 187 " --> pdb=" O ALA M 178 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA M 178 " --> pdb=" O SER M 187 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER M 189 " --> pdb=" O PHE M 176 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'M' and resid 161 through 162 Processing sheet with id=AH1, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.547A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.568A pdb=" N VAL N 11 " --> pdb=" O ASP N 105 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 114 through 118 removed outlier: 6.129A pdb=" N TYR N 173 " --> pdb=" O ASN N 138 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 146 through 150 1298 hydrogen bonds defined for protein. 3516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.64 Time building geometry restraints manager: 2.71 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: 8404 1.33 - 1.46: 7717 1.46 - 1.58: 14662 1.58 - 1.71: 0 1.71 - 1.83: 161 Bond restraints: 30944 Sorted by residual: bond pdb=" C VAL C 860 " pdb=" N LEU C 861 " ideal model delta sigma weight residual 1.331 1.248 0.083 2.07e-02 2.33e+03 1.59e+01 bond pdb=" N SER N 7 " pdb=" CA SER N 7 " ideal model delta sigma weight residual 1.453 1.485 -0.032 8.30e-03 1.45e+04 1.50e+01 bond pdb=" N SER L 7 " pdb=" CA SER L 7 " ideal model delta sigma weight residual 1.453 1.485 -0.032 9.20e-03 1.18e+04 1.20e+01 bond pdb=" CA SER B1097 " pdb=" CB SER B1097 " ideal model delta sigma weight residual 1.534 1.485 0.049 1.72e-02 3.38e+03 8.18e+00 bond pdb=" CA SER N 7 " pdb=" CB SER N 7 " ideal model delta sigma weight residual 1.536 1.504 0.032 1.23e-02 6.61e+03 6.73e+00 ... (remaining 30939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 41012 1.84 - 3.68: 1003 3.68 - 5.52: 69 5.52 - 7.36: 17 7.36 - 9.20: 2 Bond angle restraints: 42103 Sorted by residual: angle pdb=" C ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " ideal model delta sigma weight residual 116.63 110.49 6.14 1.16e+00 7.43e-01 2.80e+01 angle pdb=" C PHE C 32 " pdb=" CA PHE C 32 " pdb=" CB PHE C 32 " ideal model delta sigma weight residual 117.23 110.37 6.86 1.36e+00 5.41e-01 2.55e+01 angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 117.23 110.40 6.83 1.36e+00 5.41e-01 2.52e+01 angle pdb=" C PHE A 32 " pdb=" CA PHE A 32 " pdb=" CB PHE A 32 " ideal model delta sigma weight residual 117.23 110.44 6.79 1.36e+00 5.41e-01 2.50e+01 angle pdb=" C ASN B 87 " pdb=" CA ASN B 87 " pdb=" CB ASN B 87 " ideal model delta sigma weight residual 117.23 110.46 6.77 1.36e+00 5.41e-01 2.48e+01 ... (remaining 42098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 17529 17.68 - 35.36: 909 35.36 - 53.04: 182 53.04 - 70.72: 52 70.72 - 88.40: 31 Dihedral angle restraints: 18703 sinusoidal: 7462 harmonic: 11241 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 -178.60 -88.40 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -172.49 86.49 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 173.41 -80.41 1 1.00e+01 1.00e-02 8.00e+01 ... (remaining 18700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4278 0.072 - 0.144: 569 0.144 - 0.216: 2 0.216 - 0.289: 2 0.289 - 0.361: 2 Chirality restraints: 4853 Sorted by residual: chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 4850 not shown) Planarity restraints: 5438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN M 106 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO M 107 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO M 107 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO M 107 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 906 " -0.015 2.00e-02 2.50e+03 1.49e-02 3.90e+00 pdb=" CG PHE C 906 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE C 906 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 906 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 906 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 906 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 906 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1134 " -0.017 2.00e-02 2.50e+03 1.63e-02 3.32e+00 pdb=" CG ASN B1134 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B1134 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B1134 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG B1306 " -0.017 2.00e-02 2.50e+03 ... (remaining 5435 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1878 2.72 - 3.27: 29738 3.27 - 3.81: 49333 3.81 - 4.36: 58451 4.36 - 4.90: 102147 Nonbonded interactions: 241547 Sorted by model distance: nonbonded pdb=" O PHE A 106 " pdb=" OG SER A 116 " model vdw 2.180 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.188 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.200 3.040 nonbonded pdb=" O PHE M 29 " pdb=" NH2 ARG M 72 " model vdw 2.206 3.120 nonbonded pdb=" OD1 ASN B 439 " pdb=" OG SER B 443 " model vdw 2.207 3.040 ... (remaining 241542 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 497 or resid 499 through 1304)) selection = (chain 'B' and (resid 27 through 497 or resid 499 through 1304)) selection = (chain 'C' and (resid 27 through 379 or resid 381 through 497 or resid 499 throu \ gh 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.040 Extract box with map and model: 0.740 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 32.470 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.005 0.083 31010 Z= 0.236 Angle : 0.673 9.205 42254 Z= 0.395 Chirality : 0.045 0.361 4853 Planarity : 0.004 0.073 5421 Dihedral : 11.985 87.016 11334 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.28 % Rotamer: Outliers : 0.21 % Allowed : 0.27 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 0.02 (0.14), residues: 3817 helix: 1.43 (0.20), residues: 705 sheet: 0.49 (0.15), residues: 1085 loop : -0.77 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 38 TYR 0.020 0.001 TYR A 873 PHE 0.035 0.001 PHE C 906 TRP 0.016 0.001 TRP L 32 HIS 0.003 0.001 HIS M 100 Details of bonding type rmsd covalent geometry : bond 0.00494 (30944) covalent geometry : angle 0.66615 (42103) SS BOND : bond 0.00282 ( 47) SS BOND : angle 1.22517 ( 94) hydrogen bonds : bond 0.12506 ( 1236) hydrogen bonds : angle 6.82675 ( 3516) link_BETA1-4 : bond 0.00250 ( 2) link_BETA1-4 : angle 1.58268 ( 6) link_NAG-ASN : bond 0.00327 ( 17) link_NAG-ASN : angle 2.36434 ( 51) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 34 MET cc_start: 0.2834 (ptm) cc_final: 0.2630 (ptm) REVERT: M 104 MET cc_start: 0.5610 (tmm) cc_final: 0.5357 (tmm) outliers start: 1 outliers final: 1 residues processed: 68 average time/residue: 0.1725 time to fit residues: 20.1507 Evaluate side-chains 58 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 7 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN B 804 GLN B 935 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** H 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN M 100 HIS N 53 ASN ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 166 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 = 0.3988 r_free = 0.3988 target = 0.076813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.047638 restraints weight = 304678.432| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 8.48 r_work: 0.2800 rms_B_bonded: 6.37 restraints_weight: 2.0000 r_work: 0.2894 rms_B_bonded: 5.14 restraints_weight: 4.0000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 31010 Z= 0.121 Angle : 0.522 7.788 42254 Z= 0.277 Chirality : 0.043 0.208 4853 Planarity : 0.004 0.048 5421 Dihedral : 5.446 53.602 4535 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.38 % Favored : 96.51 % Rotamer: Outliers : 0.27 % Allowed : 1.99 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 0.30 (0.14), residues: 3817 helix: 1.97 (0.20), residues: 722 sheet: 0.60 (0.15), residues: 1092 loop : -0.69 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 328 TYR 0.027 0.001 TYR N 49 PHE 0.019 0.001 PHE C 906 TRP 0.012 0.001 TRP N 32 HIS 0.003 0.001 HIS M 174 Details of bonding type rmsd covalent geometry : bond 0.00268 (30944) covalent geometry : angle 0.51644 (42103) SS BOND : bond 0.00213 ( 47) SS BOND : angle 0.85913 ( 94) hydrogen bonds : bond 0.04624 ( 1236) hydrogen bonds : angle 5.43277 ( 3516) link_BETA1-4 : bond 0.00278 ( 2) link_BETA1-4 : angle 1.30859 ( 6) link_NAG-ASN : bond 0.00199 ( 17) link_NAG-ASN : angle 1.94120 ( 51) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8731 (ptm) cc_final: 0.8522 (ptp) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 0.1737 time to fit residues: 19.2756 Evaluate side-chains 59 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain N residue 53 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 342 optimal weight: 50.0000 chunk 60 optimal weight: 0.8980 chunk 292 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 chunk 199 optimal weight: 0.7980 chunk 269 optimal weight: 3.9990 chunk 308 optimal weight: 40.0000 chunk 268 optimal weight: 0.7980 chunk 202 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.076462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.047592 restraints weight = 282972.646| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 8.14 r_work: 0.2779 rms_B_bonded: 6.54 restraints_weight: 2.0000 r_work: 0.2871 rms_B_bonded: 5.10 restraints_weight: 4.0000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31010 Z= 0.171 Angle : 0.523 8.183 42254 Z= 0.276 Chirality : 0.043 0.217 4853 Planarity : 0.004 0.055 5421 Dihedral : 5.260 59.850 4534 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.62 % Favored : 96.28 % Rotamer: Outliers : 0.30 % Allowed : 3.21 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 0.27 (0.14), residues: 3817 helix: 2.02 (0.20), residues: 724 sheet: 0.58 (0.15), residues: 1072 loop : -0.72 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 24 TYR 0.018 0.001 TYR H 80 PHE 0.021 0.001 PHE C 906 TRP 0.009 0.001 TRP A 104 HIS 0.003 0.001 HIS M 100 Details of bonding type rmsd covalent geometry : bond 0.00391 (30944) covalent geometry : angle 0.51823 (42103) SS BOND : bond 0.00239 ( 47) SS BOND : angle 0.78991 ( 94) hydrogen bonds : bond 0.04558 ( 1236) hydrogen bonds : angle 5.26461 ( 3516) link_BETA1-4 : bond 0.00067 ( 2) link_BETA1-4 : angle 1.37008 ( 6) link_NAG-ASN : bond 0.00211 ( 17) link_NAG-ASN : angle 1.84653 ( 51) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 61 average time/residue: 0.2097 time to fit residues: 22.4249 Evaluate side-chains 60 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 117 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 35 optimal weight: 40.0000 chunk 314 optimal weight: 40.0000 chunk 226 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 275 optimal weight: 0.9990 chunk 259 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 289 optimal weight: 0.4980 chunk 278 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN H 39 GLN ** H 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 198 HIS N 53 ASN ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 166 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 = 0.3982 r_free = 0.3982 target = 0.076589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.048360 restraints weight = 267481.986| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 7.74 r_work: 0.2814 rms_B_bonded: 5.77 restraints_weight: 2.0000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31010 Z= 0.140 Angle : 0.497 7.920 42254 Z= 0.263 Chirality : 0.043 0.221 4853 Planarity : 0.004 0.056 5421 Dihedral : 4.957 56.675 4534 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.49 % Favored : 96.41 % Rotamer: Outliers : 0.30 % Allowed : 4.02 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 0.34 (0.14), residues: 3817 helix: 2.12 (0.20), residues: 724 sheet: 0.61 (0.15), residues: 1082 loop : -0.70 (0.14), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 24 TYR 0.020 0.001 TYR M 59 PHE 0.017 0.001 PHE C 906 TRP 0.009 0.001 TRP A 104 HIS 0.002 0.000 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00317 (30944) covalent geometry : angle 0.49294 (42103) SS BOND : bond 0.00253 ( 47) SS BOND : angle 0.70385 ( 94) hydrogen bonds : bond 0.04239 ( 1236) hydrogen bonds : angle 5.09718 ( 3516) link_BETA1-4 : bond 0.00154 ( 2) link_BETA1-4 : angle 1.32560 ( 6) link_NAG-ASN : bond 0.00190 ( 17) link_NAG-ASN : angle 1.76605 ( 51) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8960 (ptm) cc_final: 0.8688 (ptp) outliers start: 4 outliers final: 3 residues processed: 62 average time/residue: 0.1941 time to fit residues: 21.2530 Evaluate side-chains 61 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain N residue 117 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 263 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 262 optimal weight: 5.9990 chunk 330 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 373 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 901 GLN C 239 GLN ** H 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 166 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 = 0.3960 r_free = 0.3960 target = 0.075856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.047508 restraints weight = 237383.050| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 6.91 r_work: 0.2796 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 31010 Z= 0.261 Angle : 0.581 8.886 42254 Z= 0.304 Chirality : 0.044 0.233 4853 Planarity : 0.004 0.057 5421 Dihedral : 5.041 52.167 4534 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.33 % Rotamer: Outliers : 0.42 % Allowed : 4.43 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 0.15 (0.14), residues: 3817 helix: 1.79 (0.20), residues: 724 sheet: 0.54 (0.15), residues: 1076 loop : -0.79 (0.14), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 24 TYR 0.018 0.001 TYR N 49 PHE 0.025 0.002 PHE C 906 TRP 0.014 0.001 TRP B 64 HIS 0.005 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00596 (30944) covalent geometry : angle 0.57598 (42103) SS BOND : bond 0.00343 ( 47) SS BOND : angle 1.10723 ( 94) hydrogen bonds : bond 0.04928 ( 1236) hydrogen bonds : angle 5.29942 ( 3516) link_BETA1-4 : bond 0.00420 ( 2) link_BETA1-4 : angle 1.52055 ( 6) link_NAG-ASN : bond 0.00368 ( 17) link_NAG-ASN : angle 1.84966 ( 51) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.863 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 67 average time/residue: 0.1659 time to fit residues: 19.3783 Evaluate side-chains 61 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain M residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 362 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 249 optimal weight: 0.8980 chunk 343 optimal weight: 9.9990 chunk 297 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 373 optimal weight: 40.0000 chunk 356 optimal weight: 40.0000 chunk 162 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.076911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.048593 restraints weight = 318150.945| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 7.76 r_work: 0.2812 rms_B_bonded: 5.67 restraints_weight: 2.0000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 31010 Z= 0.097 Angle : 0.497 14.187 42254 Z= 0.261 Chirality : 0.043 0.223 4853 Planarity : 0.004 0.058 5421 Dihedral : 4.572 53.219 4534 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.62 % Rotamer: Outliers : 0.45 % Allowed : 4.73 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 0.39 (0.14), residues: 3817 helix: 2.19 (0.20), residues: 720 sheet: 0.61 (0.15), residues: 1076 loop : -0.65 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 24 TYR 0.022 0.001 TYR N 86 PHE 0.012 0.001 PHE C 906 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.000 HIS M 100 Details of bonding type rmsd covalent geometry : bond 0.00207 (30944) covalent geometry : angle 0.48866 (42103) SS BOND : bond 0.00394 ( 47) SS BOND : angle 1.58685 ( 94) hydrogen bonds : bond 0.03898 ( 1236) hydrogen bonds : angle 4.94364 ( 3516) link_BETA1-4 : bond 0.00237 ( 2) link_BETA1-4 : angle 1.34949 ( 6) link_NAG-ASN : bond 0.00236 ( 17) link_NAG-ASN : angle 1.72671 ( 51) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 873 TYR cc_start: 0.9713 (OUTLIER) cc_final: 0.9253 (m-80) outliers start: 9 outliers final: 4 residues processed: 67 average time/residue: 0.1781 time to fit residues: 21.1206 Evaluate side-chains 63 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain N residue 86 TYR Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 117 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 344 optimal weight: 40.0000 chunk 89 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 308 optimal weight: 30.0000 chunk 305 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** H 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.075802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.046257 restraints weight = 309930.151| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 8.05 r_work: 0.2775 rms_B_bonded: 6.19 restraints_weight: 2.0000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.140 31010 Z= 0.265 Angle : 0.592 14.287 42254 Z= 0.309 Chirality : 0.044 0.230 4853 Planarity : 0.004 0.055 5421 Dihedral : 4.888 52.155 4534 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.75 % Favored : 95.15 % Rotamer: Outliers : 0.51 % Allowed : 5.09 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 0.19 (0.14), residues: 3817 helix: 1.87 (0.20), residues: 721 sheet: 0.51 (0.15), residues: 1081 loop : -0.73 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 24 TYR 0.016 0.001 TYR B1067 PHE 0.024 0.002 PHE C 559 TRP 0.014 0.001 TRP B 64 HIS 0.005 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00608 (30944) covalent geometry : angle 0.58097 (42103) SS BOND : bond 0.00346 ( 47) SS BOND : angle 2.10324 ( 94) hydrogen bonds : bond 0.04865 ( 1236) hydrogen bonds : angle 5.24905 ( 3516) link_BETA1-4 : bond 0.00341 ( 2) link_BETA1-4 : angle 1.60636 ( 6) link_NAG-ASN : bond 0.00387 ( 17) link_NAG-ASN : angle 1.81831 ( 51) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 873 TYR cc_start: 0.9730 (OUTLIER) cc_final: 0.9264 (m-80) REVERT: H 34 MET cc_start: 0.3067 (mmp) cc_final: 0.2109 (mmm) outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 0.1852 time to fit residues: 22.4378 Evaluate side-chains 66 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain N residue 86 TYR Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 184 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 306 optimal weight: 30.0000 chunk 256 optimal weight: 6.9990 chunk 33 optimal weight: 30.0000 chunk 293 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 191 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.075544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.046631 restraints weight = 248445.808| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 7.56 r_work: 0.2748 rms_B_bonded: 5.96 restraints_weight: 2.0000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 31010 Z= 0.307 Angle : 0.631 14.137 42254 Z= 0.331 Chirality : 0.045 0.249 4853 Planarity : 0.004 0.054 5421 Dihedral : 5.207 52.250 4534 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.94 % Rotamer: Outliers : 0.48 % Allowed : 5.33 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: -0.02 (0.14), residues: 3817 helix: 1.59 (0.19), residues: 722 sheet: 0.41 (0.16), residues: 1076 loop : -0.84 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 24 TYR 0.019 0.002 TYR C1067 PHE 0.026 0.002 PHE B 559 TRP 0.018 0.002 TRP B 64 HIS 0.005 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00699 (30944) covalent geometry : angle 0.62156 (42103) SS BOND : bond 0.00359 ( 47) SS BOND : angle 1.97867 ( 94) hydrogen bonds : bond 0.05232 ( 1236) hydrogen bonds : angle 5.45539 ( 3516) link_BETA1-4 : bond 0.00292 ( 2) link_BETA1-4 : angle 1.58667 ( 6) link_NAG-ASN : bond 0.00449 ( 17) link_NAG-ASN : angle 1.97541 ( 51) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 873 TYR cc_start: 0.9736 (OUTLIER) cc_final: 0.9274 (m-80) REVERT: H 34 MET cc_start: 0.3269 (mmp) cc_final: 0.2248 (mmm) outliers start: 10 outliers final: 8 residues processed: 65 average time/residue: 0.1859 time to fit residues: 20.6616 Evaluate side-chains 65 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain N residue 86 TYR Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 245 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 294 optimal weight: 0.9980 chunk 241 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 302 optimal weight: 20.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.076295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.048060 restraints weight = 317057.137| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 7.56 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 31010 Z= 0.141 Angle : 0.514 10.205 42254 Z= 0.271 Chirality : 0.043 0.229 4853 Planarity : 0.004 0.056 5421 Dihedral : 4.813 52.871 4534 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 0.51 % Allowed : 5.33 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 0.21 (0.14), residues: 3817 helix: 1.96 (0.20), residues: 721 sheet: 0.49 (0.15), residues: 1090 loop : -0.75 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.017 0.001 TYR M 95 PHE 0.016 0.001 PHE C 906 TRP 0.012 0.001 TRP L 32 HIS 0.003 0.001 HIS M 100 Details of bonding type rmsd covalent geometry : bond 0.00322 (30944) covalent geometry : angle 0.50538 (42103) SS BOND : bond 0.00263 ( 47) SS BOND : angle 1.46146 ( 94) hydrogen bonds : bond 0.04370 ( 1236) hydrogen bonds : angle 5.13380 ( 3516) link_BETA1-4 : bond 0.00049 ( 2) link_BETA1-4 : angle 1.42876 ( 6) link_NAG-ASN : bond 0.00211 ( 17) link_NAG-ASN : angle 1.85373 ( 51) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 873 TYR cc_start: 0.9666 (OUTLIER) cc_final: 0.9191 (m-80) REVERT: H 34 MET cc_start: 0.5602 (mmp) cc_final: 0.3955 (mmm) outliers start: 11 outliers final: 6 residues processed: 65 average time/residue: 0.1903 time to fit residues: 21.7451 Evaluate side-chains 63 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain N residue 86 TYR Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 299 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 325 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 199 optimal weight: 0.0270 chunk 155 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 317 optimal weight: 9.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.076351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.048116 restraints weight = 317960.322| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 7.55 r_work: 0.2818 rms_B_bonded: 6.34 restraints_weight: 2.0000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31010 Z= 0.139 Angle : 0.502 9.247 42254 Z= 0.264 Chirality : 0.043 0.222 4853 Planarity : 0.004 0.056 5421 Dihedral : 4.623 52.909 4534 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 0.39 % Allowed : 5.56 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 0.32 (0.14), residues: 3817 helix: 2.11 (0.20), residues: 721 sheet: 0.53 (0.15), residues: 1097 loop : -0.67 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 24 TYR 0.017 0.001 TYR N 86 PHE 0.014 0.001 PHE C 559 TRP 0.013 0.001 TRP M 113 HIS 0.004 0.001 HIS M 112 Details of bonding type rmsd covalent geometry : bond 0.00318 (30944) covalent geometry : angle 0.49529 (42103) SS BOND : bond 0.00240 ( 47) SS BOND : angle 1.30829 ( 94) hydrogen bonds : bond 0.04153 ( 1236) hydrogen bonds : angle 5.01155 ( 3516) link_BETA1-4 : bond 0.00036 ( 2) link_BETA1-4 : angle 1.43192 ( 6) link_NAG-ASN : bond 0.00187 ( 17) link_NAG-ASN : angle 1.79879 ( 51) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 873 TYR cc_start: 0.9722 (OUTLIER) cc_final: 0.9277 (m-80) REVERT: H 34 MET cc_start: 0.4475 (mmp) cc_final: 0.3186 (mmm) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.1763 time to fit residues: 19.1520 Evaluate side-chains 63 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain N residue 86 TYR Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 133 optimal weight: 10.0000 chunk 95 optimal weight: 0.1980 chunk 6 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 384 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 313 optimal weight: 6.9990 chunk 339 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.076594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.047274 restraints weight = 322221.972| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 8.31 r_work: 0.2830 rms_B_bonded: 6.33 restraints_weight: 2.0000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31010 Z= 0.113 Angle : 0.483 8.173 42254 Z= 0.254 Chirality : 0.042 0.223 4853 Planarity : 0.004 0.061 5421 Dihedral : 4.433 52.890 4534 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 0.45 % Allowed : 5.53 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 0.42 (0.14), residues: 3817 helix: 2.28 (0.20), residues: 719 sheet: 0.56 (0.15), residues: 1108 loop : -0.63 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.016 0.001 TYR A1067 PHE 0.013 0.001 PHE C 906 TRP 0.009 0.001 TRP A 104 HIS 0.003 0.001 HIS M 100 Details of bonding type rmsd covalent geometry : bond 0.00257 (30944) covalent geometry : angle 0.47665 (42103) SS BOND : bond 0.00254 ( 47) SS BOND : angle 1.16149 ( 94) hydrogen bonds : bond 0.03855 ( 1236) hydrogen bonds : angle 4.87674 ( 3516) link_BETA1-4 : bond 0.00162 ( 2) link_BETA1-4 : angle 1.38140 ( 6) link_NAG-ASN : bond 0.00177 ( 17) link_NAG-ASN : angle 1.74951 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18575.64 seconds wall clock time: 314 minutes 38.94 seconds (18878.94 seconds total)