Starting phenix.real_space_refine on Sun Jul 5 21:58:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uz7_26881/07_2026/7uz7_26881.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uz7_26881/07_2026/7uz7_26881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uz7_26881/07_2026/7uz7_26881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uz7_26881/07_2026/7uz7_26881.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7uz7_26881/07_2026/7uz7_26881.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uz7_26881/07_2026/7uz7_26881.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uz7_26881/07_2026/7uz7_26881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uz7_26881/07_2026/7uz7_26881.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 19419 2.51 5 N 5019 2.21 5 O 5982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30552 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "M" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "N" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "P" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Q" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 6, 'TRANS': 105} 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 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 chiralities: 2 Chain: "F" 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 chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 6.49, per 1000 atoms: 0.21 Number of scatterers: 30552 At special positions: 0 Unit cell: (164.736, 161.408, 188.032, 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 132 16.00 O 5982 8.00 N 5019 7.00 C 19419 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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=2.02 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 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 104 " 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 F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 61 " " NAG A1312 " - " ASN A 122 " " NAG A1313 " - " ASN A 282 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 61 " " NAG B1312 " - " ASN B 122 " " NAG B1313 " - " ASN B 282 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 61 " " NAG C1312 " - " ASN C 122 " " NAG C1313 " - " ASN C 282 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " " NAG F 1 " - " ASN C 717 " Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.4 seconds 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7206 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 60 sheets defined 19.9% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.725A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.069A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.813A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.667A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.579A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 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 removed outlier: 3.596A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.810A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.582A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.730A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.055A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.808A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.621A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.570A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.664A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 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 984 removed outlier: 3.625A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.794A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.548A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.720A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.065A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.809A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.569A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.655A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.619A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.679A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.582A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.754A pdb=" N ASN H 36 " --> pdb=" O ASN H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'M' and resid 29 through 37 removed outlier: 3.789A pdb=" N ASN M 36 " --> pdb=" O ASN M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 99 Processing helix chain 'P' and resid 29 through 37 removed outlier: 3.742A pdb=" N ASN P 36 " --> pdb=" O ASN P 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.697A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.894A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.854A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.792A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.159A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 327 removed outlier: 4.194A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.854A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA A 435 " --> pdb=" O SER A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.854A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (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 565 through 566 removed outlier: 6.682A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.647A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.633A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.642A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.906A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.615A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.887A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.948A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.692A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.237A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 12.273A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 11.069A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 12.652A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.723A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.174A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 327 removed outlier: 4.100A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.863A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA B 435 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.863A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.638A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.661A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.187A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.720A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.838A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.735A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.517A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.111A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.858A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 435 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.858A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.637A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.561A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.735A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.970A pdb=" N GLN H 3 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 19 " --> pdb=" O LEU H 91 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 66 through 67 removed outlier: 5.082A pdb=" N TRP H 52 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY H 54 " --> pdb=" O TRP H 41 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.031A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS L 23 " --> pdb=" O PHE L 87 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE L 87 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.169A pdb=" N GLU L 125 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR L 122 " --> pdb=" O TYR L 102 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 3 through 6 removed outlier: 3.975A pdb=" N GLN M 3 " --> pdb=" O SER M 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL M 19 " --> pdb=" O LEU M 91 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 66 through 67 removed outlier: 5.087A pdb=" N TRP M 52 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS M 43 " --> pdb=" O TRP M 52 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY M 54 " --> pdb=" O TRP M 41 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.801A pdb=" N THR N 5 " --> pdb=" O LYS N 24 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.670A pdb=" N GLU N 125 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR N 122 " --> pdb=" O TYR N 102 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.984A pdb=" N GLN P 3 " --> pdb=" O SER P 26 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL P 19 " --> pdb=" O LEU P 91 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 66 through 67 removed outlier: 5.048A pdb=" N TRP P 52 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS P 43 " --> pdb=" O TRP P 52 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR P 122 " --> pdb=" O TYR P 102 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 4 through 5 removed outlier: 3.846A pdb=" N THR Q 5 " --> pdb=" O LYS Q 24 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS Q 23 " --> pdb=" O PHE Q 87 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE Q 87 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 11 through 12 removed outlier: 4.296A pdb=" N GLU Q 125 " --> pdb=" O LEU Q 11 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR Q 122 " --> pdb=" O TYR Q 102 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE Q 54 " --> pdb=" O TRP Q 41 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLN Q 43 " --> pdb=" O LEU Q 52 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU Q 52 " --> pdb=" O GLN Q 43 " (cutoff:3.500A) 1149 hydrogen bonds defined for protein. 3174 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: 7.97 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 4372 1.25 - 1.39: 8349 1.39 - 1.54: 17592 1.54 - 1.68: 773 1.68 - 1.82: 171 Bond restraints: 31257 Sorted by residual: bond pdb=" CG PRO A1079 " pdb=" CD PRO A1079 " ideal model delta sigma weight residual 1.503 1.100 0.403 3.40e-02 8.65e+02 1.40e+02 bond pdb=" CG PRO B1079 " pdb=" CD PRO B1079 " ideal model delta sigma weight residual 1.503 1.141 0.362 3.40e-02 8.65e+02 1.13e+02 bond pdb=" N PRO A1079 " pdb=" CD PRO A1079 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N PRO B1079 " pdb=" CD PRO B1079 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" N ASN C 801 " pdb=" CA ASN C 801 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 5.98e+00 ... (remaining 31252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 42537 4.49 - 8.98: 39 8.98 - 13.47: 0 13.47 - 17.96: 4 17.96 - 22.45: 2 Bond angle restraints: 42582 Sorted by residual: angle pdb=" N PRO A1079 " pdb=" CD PRO A1079 " pdb=" CG PRO A1079 " ideal model delta sigma weight residual 103.20 80.75 22.45 1.50e+00 4.44e-01 2.24e+02 angle pdb=" N PRO B1079 " pdb=" CD PRO B1079 " pdb=" CG PRO B1079 " ideal model delta sigma weight residual 103.20 82.34 20.86 1.50e+00 4.44e-01 1.93e+02 angle pdb=" CA PRO B1079 " pdb=" N PRO B1079 " pdb=" CD PRO B1079 " ideal model delta sigma weight residual 112.00 97.65 14.35 1.40e+00 5.10e-01 1.05e+02 angle pdb=" CA PRO A1079 " pdb=" N PRO A1079 " pdb=" CD PRO A1079 " ideal model delta sigma weight residual 112.00 98.42 13.58 1.40e+00 5.10e-01 9.41e+01 angle pdb=" CA PRO A1079 " pdb=" CB PRO A1079 " pdb=" CG PRO A1079 " ideal model delta sigma weight residual 104.50 89.34 15.16 1.90e+00 2.77e-01 6.37e+01 ... (remaining 42577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 16693 17.50 - 34.99: 1226 34.99 - 52.49: 214 52.49 - 69.98: 30 69.98 - 87.48: 35 Dihedral angle restraints: 18198 sinusoidal: 6975 harmonic: 11223 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 104 " pdb=" CB CYS L 104 " ideal model delta sinusoidal sigma weight residual 93.00 167.97 -74.97 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 104 " pdb=" CB CYS N 104 " ideal model delta sinusoidal sigma weight residual 93.00 163.23 -70.23 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CB CYS Q 23 " pdb=" SG CYS Q 23 " pdb=" SG CYS Q 104 " pdb=" CB CYS Q 104 " ideal model delta sinusoidal sigma weight residual 93.00 154.84 -61.84 1 1.00e+01 1.00e-02 5.07e+01 ... (remaining 18195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4130 0.058 - 0.115: 747 0.115 - 0.173: 63 0.173 - 0.231: 3 0.231 - 0.289: 1 Chirality restraints: 4944 Sorted by residual: chirality pdb=" C1 NAG A1312 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1312 " pdb=" O5 NAG A1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" C1 NAG B1311 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1311 " pdb=" O5 NAG B1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.35e-01 ... (remaining 4941 not shown) Planarity restraints: 5499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " 0.228 2.00e-02 2.50e+03 1.95e-01 4.75e+02 pdb=" C7 NAG A1307 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.152 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " -0.334 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " -0.226 2.00e-02 2.50e+03 1.93e-01 4.65e+02 pdb=" C7 NAG B1307 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " -0.151 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " 0.330 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1307 " -0.222 2.00e-02 2.50e+03 1.89e-01 4.49e+02 pdb=" C7 NAG C1307 " 0.055 2.00e-02 2.50e+03 pdb=" C8 NAG C1307 " -0.149 2.00e-02 2.50e+03 pdb=" N2 NAG C1307 " 0.324 2.00e-02 2.50e+03 pdb=" O7 NAG C1307 " -0.008 2.00e-02 2.50e+03 ... (remaining 5496 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 521 2.68 - 3.23: 29270 3.23 - 3.79: 47533 3.79 - 4.34: 65317 4.34 - 4.90: 107380 Nonbonded interactions: 250021 Sorted by model distance: nonbonded pdb=" O ARG A 214 " pdb=" OH TYR A 266 " model vdw 2.121 3.040 nonbonded pdb=" NZ LYS C 811 " pdb=" OD2 ASP C 820 " model vdw 2.179 3.120 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.195 3.040 nonbonded pdb=" OE1 GLN B 804 " pdb=" NE2 GLN B 935 " model vdw 2.205 3.120 nonbonded pdb=" OH TYR B 369 " pdb=" O PRO B 384 " model vdw 2.209 3.040 ... (remaining 250016 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 29.090 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 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 0.403 31344 Z= 0.189 Angle : 0.620 22.452 42801 Z= 0.330 Chirality : 0.044 0.289 4944 Planarity : 0.006 0.195 5457 Dihedral : 12.961 87.476 10866 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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 are not related in a simple way. whole: 0.04 (0.14), residues: 3813 helix: 1.79 (0.21), residues: 672 sheet: 0.32 (0.17), residues: 888 loop : -0.64 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.025 0.001 TYR B 248 PHE 0.023 0.001 PHE A 906 TRP 0.033 0.001 TRP C 104 HIS 0.002 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (31257) covalent geometry : angle 0.60739 / 0.33 (42582) SS BOND : bond 0.00313 / 0.18 ( 42) SS BOND : angle 0.92101 / 0.68 ( 84) hydrogen bonds : bond 0.21353 / 14.31 ( 1074) hydrogen bonds : angle 9.00623 / 6.23 ( 3174) link_BETA1-4 : bond 0.00284 / 0.18 ( 3) link_BETA1-4 : angle 1.47864 / 0.99 ( 9) link_NAG-ASN : bond 0.00471 / 0.32 ( 42) link_NAG-ASN : angle 2.24448 / 1.40 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6905 (m-90) cc_final: 0.6688 (m-90) REVERT: A 120 VAL cc_start: 0.7684 (t) cc_final: 0.7454 (m) REVERT: B 104 TRP cc_start: 0.7650 (m-90) cc_final: 0.7262 (m-90) REVERT: B 265 TYR cc_start: 0.7589 (p90) cc_final: 0.7309 (p90) REVERT: N 4 MET cc_start: 0.2404 (tpt) cc_final: 0.2153 (tpt) REVERT: N 122 THR cc_start: 0.1325 (p) cc_final: 0.0575 (p) REVERT: Q 4 MET cc_start: 0.2405 (tpp) cc_final: 0.2165 (tpp) outliers start: 0 outliers final: 1 residues processed: 244 average time/residue: 0.6039 time to fit residues: 178.6826 Evaluate side-chains 154 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 702 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 957 GLN B1010 GLN C 239 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1010 GLN H 6 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.232577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.161624 restraints weight = 44399.901| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 3.76 r_work: 0.3330 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 31344 Z= 0.221 Angle : 0.645 12.663 42801 Z= 0.326 Chirality : 0.047 0.281 4944 Planarity : 0.004 0.055 5457 Dihedral : 4.303 28.127 4140 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.73 % Allowed : 8.96 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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 are not related in a simple way. whole: -0.06 (0.13), residues: 3813 helix: 1.53 (0.21), residues: 657 sheet: 0.44 (0.18), residues: 852 loop : -0.70 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 237 TYR 0.025 0.002 TYR B1067 PHE 0.027 0.002 PHE C1121 TRP 0.023 0.001 TRP C 104 HIS 0.005 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (31257) covalent geometry : angle 0.63214 / 0.32 (42582) SS BOND : bond 0.00594 / 0.37 ( 42) SS BOND : angle 1.15025 / 0.82 ( 84) hydrogen bonds : bond 0.04655 / 3.07 ( 1074) hydrogen bonds : angle 6.64112 / 4.57 ( 3174) link_BETA1-4 : bond 0.00068 / 0.04 ( 3) link_BETA1-4 : angle 1.64103 / 1.07 ( 9) link_NAG-ASN : bond 0.00477 / 0.32 ( 42) link_NAG-ASN : angle 2.24891 / 1.50 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 265 TYR cc_start: 0.7158 (p90) cc_final: 0.6724 (p90) REVERT: C 190 ARG cc_start: 0.6906 (mtp-110) cc_final: 0.6656 (mmt90) REVERT: C 820 ASP cc_start: 0.7317 (m-30) cc_final: 0.7037 (m-30) REVERT: C 1029 MET cc_start: 0.8162 (tpp) cc_final: 0.7840 (tpp) REVERT: N 4 MET cc_start: 0.4592 (tpt) cc_final: 0.4171 (tpt) REVERT: Q 4 MET cc_start: 0.4466 (tpp) cc_final: 0.4098 (mmm) outliers start: 24 outliers final: 12 residues processed: 188 average time/residue: 0.5103 time to fit residues: 119.2037 Evaluate side-chains 157 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 314 optimal weight: 0.0000 chunk 230 optimal weight: 9.9990 chunk 310 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 43 optimal weight: 50.0000 chunk 64 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 288 optimal weight: 0.9980 chunk 315 optimal weight: 50.0000 chunk 177 optimal weight: 0.5980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.234252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.163598 restraints weight = 44475.604| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 3.72 r_work: 0.3368 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 31344 Z= 0.123 Angle : 0.567 12.535 42801 Z= 0.284 Chirality : 0.045 0.278 4944 Planarity : 0.004 0.049 5457 Dihedral : 4.078 24.134 4137 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.00 % Allowed : 11.23 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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 are not related in a simple way. whole: 0.05 (0.13), residues: 3813 helix: 1.85 (0.20), residues: 669 sheet: 0.47 (0.18), residues: 840 loop : -0.70 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 190 TYR 0.022 0.001 TYR A 170 PHE 0.015 0.001 PHE A1121 TRP 0.014 0.001 TRP C 104 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (31257) covalent geometry : angle 0.55539 / 0.28 (42582) SS BOND : bond 0.00296 / 0.18 ( 42) SS BOND : angle 0.86584 / 0.60 ( 84) hydrogen bonds : bond 0.03976 / 2.64 ( 1074) hydrogen bonds : angle 5.97584 / 4.10 ( 3174) link_BETA1-4 : bond 0.00200 / 0.13 ( 3) link_BETA1-4 : angle 1.29101 / 0.87 ( 9) link_NAG-ASN : bond 0.00476 / 0.33 ( 42) link_NAG-ASN : angle 2.11031 / 1.41 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 265 TYR cc_start: 0.6973 (p90) cc_final: 0.6511 (p90) REVERT: C 177 MET cc_start: 0.7195 (mpt) cc_final: 0.6929 (tpt) REVERT: C 190 ARG cc_start: 0.6796 (mtp-110) cc_final: 0.6585 (mmt90) REVERT: C 1029 MET cc_start: 0.8104 (tpp) cc_final: 0.7894 (tpp) REVERT: N 4 MET cc_start: 0.4356 (tpt) cc_final: 0.3931 (tpt) REVERT: N 38 TYR cc_start: 0.5559 (m-10) cc_final: 0.5347 (m-10) REVERT: Q 4 MET cc_start: 0.4382 (tpp) cc_final: 0.4008 (mmm) outliers start: 33 outliers final: 16 residues processed: 188 average time/residue: 0.5218 time to fit residues: 122.3741 Evaluate side-chains 162 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 980 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 141 optimal weight: 20.0000 chunk 292 optimal weight: 2.9990 chunk 245 optimal weight: 40.0000 chunk 269 optimal weight: 1.9990 chunk 366 optimal weight: 20.0000 chunk 349 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 290 optimal weight: 2.9990 chunk 275 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 136 optimal weight: 30.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.232107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.160028 restraints weight = 44131.525| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.66 r_work: 0.3323 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31344 Z= 0.202 Angle : 0.607 12.487 42801 Z= 0.304 Chirality : 0.046 0.284 4944 Planarity : 0.004 0.042 5457 Dihedral : 4.208 24.944 4137 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.12 % Allowed : 12.62 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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 are not related in a simple way. whole: -0.08 (0.13), residues: 3813 helix: 1.54 (0.20), residues: 678 sheet: 0.30 (0.17), residues: 900 loop : -0.71 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 983 TYR 0.022 0.001 TYR B1067 PHE 0.026 0.002 PHE B1121 TRP 0.011 0.001 TRP C 886 HIS 0.006 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (31257) covalent geometry : angle 0.59230 / 0.30 (42582) SS BOND : bond 0.00575 / 0.35 ( 42) SS BOND : angle 1.10978 / 0.84 ( 84) hydrogen bonds : bond 0.03999 / 2.64 ( 1074) hydrogen bonds : angle 5.88814 / 4.04 ( 3174) link_BETA1-4 : bond 0.00102 / 0.07 ( 3) link_BETA1-4 : angle 1.66262 / 1.11 ( 9) link_NAG-ASN : bond 0.00495 / 0.33 ( 42) link_NAG-ASN : angle 2.36773 / 1.58 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 153 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ASN cc_start: 0.5496 (p0) cc_final: 0.5191 (p0) REVERT: B 235 ILE cc_start: 0.6598 (tp) cc_final: 0.6352 (tt) REVERT: C 177 MET cc_start: 0.7120 (mpt) cc_final: 0.6919 (tpt) REVERT: C 190 ARG cc_start: 0.6821 (mtp-110) cc_final: 0.6591 (mmt90) REVERT: C 319 ARG cc_start: 0.8072 (ttm170) cc_final: 0.7381 (ttm-80) REVERT: C 697 MET cc_start: 0.8487 (ptt) cc_final: 0.8231 (ptm) REVERT: N 4 MET cc_start: 0.4550 (tpt) cc_final: 0.4140 (tpt) REVERT: Q 4 MET cc_start: 0.4583 (tpp) cc_final: 0.4175 (mmm) outliers start: 70 outliers final: 35 residues processed: 213 average time/residue: 0.4648 time to fit residues: 123.6431 Evaluate side-chains 179 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 104 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 82 optimal weight: 0.5980 chunk 217 optimal weight: 6.9990 chunk 180 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 282 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 239 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.233572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.163158 restraints weight = 44066.344| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 3.74 r_work: 0.3346 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.003 0.043 31344 Z= 0.128 Angle : 0.562 12.458 42801 Z= 0.280 Chirality : 0.045 0.283 4944 Planarity : 0.004 0.038 5457 Dihedral : 4.079 28.780 4137 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.79 % Allowed : 13.99 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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 are not related in a simple way. whole: -0.00 (0.13), residues: 3813 helix: 1.74 (0.20), residues: 678 sheet: 0.47 (0.17), residues: 855 loop : -0.75 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 983 TYR 0.025 0.001 TYR C 170 PHE 0.017 0.001 PHE A1121 TRP 0.011 0.001 TRP C 886 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (31257) covalent geometry : angle 0.54881 / 0.28 (42582) SS BOND : bond 0.00358 / 0.22 ( 42) SS BOND : angle 0.89478 / 0.65 ( 84) hydrogen bonds : bond 0.03642 / 2.40 ( 1074) hydrogen bonds : angle 5.57642 / 3.82 ( 3174) link_BETA1-4 : bond 0.00136 / 0.09 ( 3) link_BETA1-4 : angle 1.36647 / 0.92 ( 9) link_NAG-ASN : bond 0.00417 / 0.29 ( 42) link_NAG-ASN : angle 2.15862 / 1.43 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 150 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.6668 (tp) cc_final: 0.6460 (tt) REVERT: B 265 TYR cc_start: 0.6987 (p90) cc_final: 0.6504 (p90) REVERT: B 1092 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7471 (pt0) REVERT: C 319 ARG cc_start: 0.8034 (ttm170) cc_final: 0.7431 (ttm-80) REVERT: C 1029 MET cc_start: 0.8125 (tpp) cc_final: 0.7826 (tpp) REVERT: N 4 MET cc_start: 0.3974 (tpt) cc_final: 0.3600 (tpt) REVERT: Q 4 MET cc_start: 0.4154 (tpp) cc_final: 0.3746 (mmm) outliers start: 59 outliers final: 35 residues processed: 203 average time/residue: 0.5064 time to fit residues: 127.8071 Evaluate side-chains 178 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 22 optimal weight: 30.0000 chunk 139 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 332 optimal weight: 30.0000 chunk 101 optimal weight: 2.9990 chunk 281 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 376 optimal weight: 3.9990 chunk 140 optimal weight: 40.0000 chunk 188 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A1011 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B 957 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN M 117 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.231558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.160196 restraints weight = 44085.466| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.76 r_work: 0.3296 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31344 Z= 0.211 Angle : 0.606 12.337 42801 Z= 0.303 Chirality : 0.046 0.294 4944 Planarity : 0.004 0.041 5457 Dihedral : 4.244 29.919 4137 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.21 % Allowed : 14.50 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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 are not related in a simple way. whole: -0.14 (0.13), residues: 3813 helix: 1.49 (0.20), residues: 678 sheet: 0.23 (0.16), residues: 954 loop : -0.76 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.026 0.001 TYR C 170 PHE 0.028 0.002 PHE B1121 TRP 0.011 0.001 TRP C 886 HIS 0.005 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (31257) covalent geometry : angle 0.59124 / 0.30 (42582) SS BOND : bond 0.00615 / 0.38 ( 42) SS BOND : angle 1.04881 / 0.77 ( 84) hydrogen bonds : bond 0.03908 / 2.57 ( 1074) hydrogen bonds : angle 5.65792 / 3.89 ( 3174) link_BETA1-4 : bond 0.00141 / 0.08 ( 3) link_BETA1-4 : angle 1.79409 / 1.20 ( 9) link_NAG-ASN : bond 0.00484 / 0.33 ( 42) link_NAG-ASN : angle 2.38032 / 1.60 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 154 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7648 (mtm-85) REVERT: A 281 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7457 (pp20) REVERT: B 122 ASN cc_start: 0.5718 (p0) cc_final: 0.5422 (p0) REVERT: C 177 MET cc_start: 0.6580 (tpt) cc_final: 0.5971 (mmt) REVERT: C 558 LYS cc_start: 0.8291 (mmtm) cc_final: 0.8020 (mmtm) REVERT: C 697 MET cc_start: 0.8456 (ptt) cc_final: 0.8149 (ptm) REVERT: C 1029 MET cc_start: 0.8218 (tpp) cc_final: 0.7901 (tpp) REVERT: N 4 MET cc_start: 0.4414 (tpt) cc_final: 0.4031 (tpt) REVERT: Q 4 MET cc_start: 0.4648 (tpp) cc_final: 0.4152 (mmm) outliers start: 73 outliers final: 45 residues processed: 216 average time/residue: 0.4868 time to fit residues: 131.6756 Evaluate side-chains 189 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 297 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 chunk 349 optimal weight: 0.0770 chunk 13 optimal weight: 20.0000 chunk 253 optimal weight: 5.9990 chunk 315 optimal weight: 40.0000 chunk 27 optimal weight: 0.0770 chunk 107 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 324 optimal weight: 50.0000 chunk 270 optimal weight: 0.6980 overall best weight: 0.9698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN B 81 ASN B 196 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.233911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.144857 restraints weight = 43635.240| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.64 r_work: 0.3332 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31344 Z= 0.124 Angle : 0.561 12.326 42801 Z= 0.280 Chirality : 0.045 0.293 4944 Planarity : 0.004 0.039 5457 Dihedral : 4.083 30.303 4137 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.85 % Allowed : 15.44 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.13), residues: 3813 helix: 1.75 (0.20), residues: 678 sheet: 0.35 (0.17), residues: 903 loop : -0.73 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 983 TYR 0.025 0.001 TYR C 170 PHE 0.017 0.001 PHE A1121 TRP 0.011 0.001 TRP C 886 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (31257) covalent geometry : angle 0.54813 / 0.28 (42582) SS BOND : bond 0.00340 / 0.21 ( 42) SS BOND : angle 0.85122 / 0.62 ( 84) hydrogen bonds : bond 0.03533 / 2.33 ( 1074) hydrogen bonds : angle 5.41119 / 3.70 ( 3174) link_BETA1-4 : bond 0.00210 / 0.13 ( 3) link_BETA1-4 : angle 1.35653 / 0.91 ( 9) link_NAG-ASN : bond 0.00447 / 0.30 ( 42) link_NAG-ASN : angle 2.15319 / 1.43 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 155 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7638 (mtm-85) REVERT: A 281 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7491 (pp20) REVERT: A 574 ASP cc_start: 0.7551 (t0) cc_final: 0.7214 (t0) REVERT: B 122 ASN cc_start: 0.5648 (p0) cc_final: 0.5408 (p0) REVERT: B 702 GLU cc_start: 0.8308 (mp0) cc_final: 0.8058 (OUTLIER) REVERT: B 745 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.7895 (p0) REVERT: B 1092 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7394 (pt0) REVERT: C 574 ASP cc_start: 0.7661 (t0) cc_final: 0.7203 (t0) REVERT: C 675 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 787 GLN cc_start: 0.8225 (mt0) cc_final: 0.7963 (mt0) REVERT: C 1029 MET cc_start: 0.8071 (tpp) cc_final: 0.7811 (tpp) REVERT: N 4 MET cc_start: 0.5183 (tpt) cc_final: 0.4818 (tpt) REVERT: Q 4 MET cc_start: 0.5166 (tpp) cc_final: 0.4644 (mmm) outliers start: 61 outliers final: 39 residues processed: 211 average time/residue: 0.5258 time to fit residues: 138.7842 Evaluate side-chains 186 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 224 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 352 optimal weight: 40.0000 chunk 34 optimal weight: 7.9990 chunk 182 optimal weight: 0.0010 chunk 310 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 0.2980 chunk 368 optimal weight: 20.0000 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.234852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.147674 restraints weight = 43641.582| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.86 r_work: 0.3350 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31344 Z= 0.106 Angle : 0.547 12.385 42801 Z= 0.272 Chirality : 0.044 0.293 4944 Planarity : 0.003 0.040 5457 Dihedral : 3.954 29.707 4137 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.79 % Allowed : 15.41 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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 are not related in a simple way. whole: 0.11 (0.13), residues: 3813 helix: 1.94 (0.20), residues: 681 sheet: 0.48 (0.17), residues: 864 loop : -0.69 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 158 TYR 0.024 0.001 TYR A 170 PHE 0.015 0.001 PHE A1121 TRP 0.009 0.001 TRP C 886 HIS 0.001 0.000 HIS M 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (31257) covalent geometry : angle 0.53539 / 0.27 (42582) SS BOND : bond 0.00304 / 0.19 ( 42) SS BOND : angle 0.80910 / 0.60 ( 84) hydrogen bonds : bond 0.03376 / 2.23 ( 1074) hydrogen bonds : angle 5.21775 / 3.57 ( 3174) link_BETA1-4 : bond 0.00276 / 0.18 ( 3) link_BETA1-4 : angle 1.12619 / 0.76 ( 9) link_NAG-ASN : bond 0.00410 / 0.29 ( 42) link_NAG-ASN : angle 2.06252 / 1.35 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 160 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7450 (pp20) REVERT: A 574 ASP cc_start: 0.7508 (t0) cc_final: 0.7157 (t0) REVERT: A 1092 GLU cc_start: 0.8326 (tp30) cc_final: 0.7420 (pt0) REVERT: B 702 GLU cc_start: 0.8320 (mp0) cc_final: 0.8033 (OUTLIER) REVERT: B 745 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.7828 (p0) REVERT: B 988 GLU cc_start: 0.8061 (mp0) cc_final: 0.7792 (mp0) REVERT: B 1092 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7390 (pt0) REVERT: C 177 MET cc_start: 0.6931 (tpt) cc_final: 0.5995 (mmt) REVERT: C 675 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7626 (tm-30) REVERT: C 697 MET cc_start: 0.8302 (ptt) cc_final: 0.8025 (ptm) REVERT: C 787 GLN cc_start: 0.8204 (mt0) cc_final: 0.7947 (mt0) REVERT: C 1029 MET cc_start: 0.8029 (tpp) cc_final: 0.7684 (tpp) REVERT: L 4 MET cc_start: 0.4890 (tpt) cc_final: 0.4669 (tpt) REVERT: N 4 MET cc_start: 0.5229 (tpt) cc_final: 0.4860 (tpt) REVERT: P 39 MET cc_start: 0.3467 (ptm) cc_final: 0.3062 (ttp) REVERT: Q 4 MET cc_start: 0.5258 (tpp) cc_final: 0.4750 (mmm) REVERT: Q 116 LEU cc_start: 0.0081 (OUTLIER) cc_final: -0.0267 (pp) outliers start: 59 outliers final: 34 residues processed: 213 average time/residue: 0.5101 time to fit residues: 136.0544 Evaluate side-chains 179 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 376 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 348 optimal weight: 5.9990 chunk 333 optimal weight: 40.0000 chunk 8 optimal weight: 20.0000 chunk 190 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 chunk 281 optimal weight: 0.8980 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.232592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.141385 restraints weight = 44214.353| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.72 r_work: 0.3307 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31344 Z= 0.163 Angle : 0.585 12.356 42801 Z= 0.289 Chirality : 0.045 0.301 4944 Planarity : 0.004 0.039 5457 Dihedral : 4.045 29.077 4137 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.54 % Allowed : 16.02 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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 are not related in a simple way. whole: 0.03 (0.13), residues: 3813 helix: 1.79 (0.20), residues: 678 sheet: 0.47 (0.17), residues: 864 loop : -0.72 (0.13), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 983 TYR 0.020 0.001 TYR A 170 PHE 0.023 0.001 PHE B1121 TRP 0.008 0.001 TRP C 886 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (31257) covalent geometry : angle 0.57281 / 0.29 (42582) SS BOND : bond 0.00523 / 0.29 ( 42) SS BOND : angle 0.93574 / 0.68 ( 84) hydrogen bonds : bond 0.03556 / 2.34 ( 1074) hydrogen bonds : angle 5.30131 / 3.63 ( 3174) link_BETA1-4 : bond 0.00080 / 0.05 ( 3) link_BETA1-4 : angle 1.44763 / 0.97 ( 9) link_NAG-ASN : bond 0.00425 / 0.30 ( 42) link_NAG-ASN : angle 2.14920 / 1.42 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7637 (mtm-85) REVERT: A 281 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7423 (pp20) REVERT: A 574 ASP cc_start: 0.7534 (t0) cc_final: 0.7170 (t0) REVERT: A 1092 GLU cc_start: 0.8297 (tp30) cc_final: 0.7376 (pt0) REVERT: B 122 ASN cc_start: 0.5666 (p0) cc_final: 0.5423 (p0) REVERT: B 702 GLU cc_start: 0.8347 (mp0) cc_final: 0.8073 (OUTLIER) REVERT: B 745 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.7888 (p0) REVERT: B 988 GLU cc_start: 0.8048 (mp0) cc_final: 0.7793 (mp0) REVERT: B 1092 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7377 (pt0) REVERT: C 177 MET cc_start: 0.6894 (tpt) cc_final: 0.6627 (tpt) REVERT: C 190 ARG cc_start: 0.7179 (mtm110) cc_final: 0.6262 (mmt90) REVERT: C 675 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7640 (tm-30) REVERT: C 787 GLN cc_start: 0.8250 (mt0) cc_final: 0.8009 (mt0) REVERT: C 1029 MET cc_start: 0.8148 (tpp) cc_final: 0.7768 (tpp) REVERT: L 4 MET cc_start: 0.4846 (tpt) cc_final: 0.4613 (tpt) REVERT: N 4 MET cc_start: 0.5172 (tpt) cc_final: 0.4795 (tpt) REVERT: P 39 MET cc_start: 0.3610 (ptm) cc_final: 0.3253 (ttp) REVERT: Q 4 MET cc_start: 0.5197 (tpp) cc_final: 0.4699 (mmm) REVERT: Q 116 LEU cc_start: 0.0087 (OUTLIER) cc_final: -0.0263 (pp) outliers start: 51 outliers final: 34 residues processed: 196 average time/residue: 0.4999 time to fit residues: 122.0269 Evaluate side-chains 180 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 108 optimal weight: 7.9990 chunk 152 optimal weight: 50.0000 chunk 109 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 338 optimal weight: 10.0000 chunk 199 optimal weight: 0.5980 chunk 244 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 245 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.231889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.140257 restraints weight = 43971.222| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.70 r_work: 0.3290 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31344 Z= 0.184 Angle : 0.603 13.265 42801 Z= 0.300 Chirality : 0.046 0.315 4944 Planarity : 0.004 0.042 5457 Dihedral : 4.159 28.911 4137 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.33 % Allowed : 16.26 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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 are not related in a simple way. whole: -0.05 (0.13), residues: 3813 helix: 1.62 (0.20), residues: 678 sheet: 0.39 (0.17), residues: 909 loop : -0.75 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 983 TYR 0.024 0.001 TYR C 170 PHE 0.024 0.001 PHE B1121 TRP 0.011 0.001 TRP C 886 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (31257) covalent geometry : angle 0.59048 / 0.30 (42582) SS BOND : bond 0.00534 / 0.33 ( 42) SS BOND : angle 0.97218 / 0.71 ( 84) hydrogen bonds : bond 0.03680 / 2.43 ( 1074) hydrogen bonds : angle 5.38234 / 3.69 ( 3174) link_BETA1-4 : bond 0.00058 / 0.03 ( 3) link_BETA1-4 : angle 1.67107 / 1.11 ( 9) link_NAG-ASN : bond 0.00432 / 0.30 ( 42) link_NAG-ASN : angle 2.23499 / 1.49 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7472 (ppp) cc_final: 0.5153 (mpp) REVERT: A 190 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7639 (mtm-85) REVERT: A 281 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7409 (pp20) REVERT: A 574 ASP cc_start: 0.7574 (t0) cc_final: 0.7207 (t0) REVERT: A 1092 GLU cc_start: 0.8302 (tp30) cc_final: 0.7379 (pt0) REVERT: B 122 ASN cc_start: 0.5704 (p0) cc_final: 0.5441 (p0) REVERT: B 745 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.7978 (p0) REVERT: B 787 GLN cc_start: 0.8246 (mt0) cc_final: 0.7777 (tt0) REVERT: B 988 GLU cc_start: 0.8066 (mp0) cc_final: 0.7814 (mp0) REVERT: B 1092 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7379 (pt0) REVERT: C 675 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 787 GLN cc_start: 0.8270 (mt0) cc_final: 0.8002 (mt0) REVERT: C 1029 MET cc_start: 0.8150 (tpp) cc_final: 0.7830 (tpp) REVERT: L 4 MET cc_start: 0.4959 (tpt) cc_final: 0.4721 (tpt) REVERT: N 4 MET cc_start: 0.5276 (tpt) cc_final: 0.4903 (tpt) REVERT: P 39 MET cc_start: 0.3592 (ptm) cc_final: 0.3251 (ttp) REVERT: Q 4 MET cc_start: 0.5268 (tpp) cc_final: 0.4760 (mmm) REVERT: Q 116 LEU cc_start: 0.0281 (OUTLIER) cc_final: -0.0077 (pp) outliers start: 44 outliers final: 33 residues processed: 189 average time/residue: 0.5037 time to fit residues: 119.3816 Evaluate side-chains 178 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 81 optimal weight: 0.5980 chunk 307 optimal weight: 0.6980 chunk 254 optimal weight: 10.0000 chunk 156 optimal weight: 0.1980 chunk 363 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 chunk 308 optimal weight: 0.7980 chunk 266 optimal weight: 0.9990 chunk 43 optimal weight: 50.0000 chunk 240 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.233795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.143617 restraints weight = 44320.722| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.70 r_work: 0.3339 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31344 Z= 0.112 Angle : 0.565 13.012 42801 Z= 0.279 Chirality : 0.044 0.312 4944 Planarity : 0.004 0.039 5457 Dihedral : 3.989 28.823 4137 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.18 % Allowed : 16.35 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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 are not related in a simple way. whole: 0.07 (0.13), residues: 3813 helix: 1.85 (0.20), residues: 678 sheet: 0.53 (0.17), residues: 858 loop : -0.72 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG C 983 TYR 0.023 0.001 TYR A 170 PHE 0.015 0.001 PHE A1121 TRP 0.010 0.001 TRP C 886 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (31257) covalent geometry : angle 0.55343 / 0.28 (42582) SS BOND : bond 0.00270 / 0.16 ( 42) SS BOND : angle 0.82211 / 0.59 ( 84) hydrogen bonds : bond 0.03364 / 2.23 ( 1074) hydrogen bonds : angle 5.15673 / 3.53 ( 3174) link_BETA1-4 : bond 0.00240 / 0.16 ( 3) link_BETA1-4 : angle 1.17639 / 0.77 ( 9) link_NAG-ASN : bond 0.00412 / 0.29 ( 42) link_NAG-ASN : angle 2.06531 / 1.36 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14586.35 seconds wall clock time: 248 minutes 21.10 seconds (14901.10 seconds total)