Starting phenix.real_space_refine on Sun Jul 5 10:49:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gou_34181/07_2026/8gou_34181.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gou_34181/07_2026/8gou_34181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8gou_34181/07_2026/8gou_34181.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gou_34181/07_2026/8gou_34181.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gou_34181/07_2026/8gou_34181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gou_34181/07_2026/8gou_34181.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gou_34181/07_2026/8gou_34181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gou_34181/07_2026/8gou_34181.map" } resolution = 3.7 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 17316 2.51 5 N 4467 2.21 5 O 5202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 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: 27108 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7754 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 9, 'ASN:plan1': 6, 'GLU:plan': 7, 'PHE:plan': 2, 'ARG:plan': 5, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 157 Chain: "B" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7705 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 7, 'GLU:plan': 8, 'PHE:plan': 3, 'ARG:plan': 5, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 187 Chain: "C" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7705 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 7, 'GLU:plan': 8, 'PHE:plan': 3, 'ARG:plan': 5, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 187 Chain: "I" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 915 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "J" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 798 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 915 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "K" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 798 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 6.37, per 1000 atoms: 0.23 Number of scatterers: 27108 At special positions: 0 Unit cell: (142.68, 200.9, 180.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 123 16.00 O 5202 8.00 N 4467 7.00 C 17316 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=2.04 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 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.01 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.1 seconds 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6554 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 56 sheets defined 22.6% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.654A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.516A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.497A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.507A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.783A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.667A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.902A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.621A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.996A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.090A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1140 through 1145' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.786A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.559A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.822A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.020A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.026A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1140 through 1145' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.543A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.595A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.574A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.699A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.565A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.502A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.092A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.880A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 81 through 85 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 8.684A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.652A 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: 6.423A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.183A 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: 3.751A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.414A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.433A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.754A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.937A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.235A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (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 728 removed outlier: 7.047A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A1052 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.047A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.099A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.402A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 8.601A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.232A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.983A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.266A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.585A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.838A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.684A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.242A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.993A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.993A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.542A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.457A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.501A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 63 through 66 removed outlier: 3.601A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.564A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.198A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 376 through 380 Processing sheet with id=AE2, first strand: chain 'C' and resid 423 through 424 removed outlier: 4.421A pdb=" N LYS C 424 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU C 465 " --> pdb=" O LYS C 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.214A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.915A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.915A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.445A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.408A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 7 removed outlier: 5.148A pdb=" N GLY I 16 " --> pdb=" O SER I 85 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.155A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AF3, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.281A pdb=" N GLN J 39 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU J 48 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AF5, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AF6, first strand: chain 'H' and resid 3 through 7 removed outlier: 5.517A pdb=" N GLY H 16 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.210A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF9, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.555A pdb=" N GLN K 39 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU K 48 " --> pdb=" O GLN K 39 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 9 through 12 Processing sheet with id=AG2, first strand: chain 'K' and resid 18 through 23 1139 hydrogen bonds defined for protein. 3018 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.93 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 8650 1.34 - 1.48: 7601 1.48 - 1.62: 11339 1.62 - 1.76: 8 1.76 - 1.90: 147 Bond restraints: 27745 Sorted by residual: bond pdb=" C PRO A 862 " pdb=" O PRO A 862 " ideal model delta sigma weight residual 1.240 1.205 0.035 1.12e-02 7.97e+03 9.86e+00 bond pdb=" N LEU A 117 " pdb=" CA LEU A 117 " ideal model delta sigma weight residual 1.454 1.490 -0.037 1.23e-02 6.61e+03 8.87e+00 bond pdb=" N GLU A 583 " pdb=" CA GLU A 583 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.19e-02 7.06e+03 7.69e+00 bond pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 1.808 1.900 -0.092 3.30e-02 9.18e+02 7.69e+00 bond pdb=" N PHE A 377 " pdb=" CA PHE A 377 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.08e-02 8.57e+03 7.19e+00 ... (remaining 27740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 36798 2.52 - 5.05: 959 5.05 - 7.57: 91 7.57 - 10.09: 26 10.09 - 12.62: 3 Bond angle restraints: 37877 Sorted by residual: angle pdb=" CA CYS B 538 " pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " ideal model delta sigma weight residual 114.40 127.02 -12.62 2.30e+00 1.89e-01 3.01e+01 angle pdb=" N TYR K 51 " pdb=" CA TYR K 51 " pdb=" C TYR K 51 " ideal model delta sigma weight residual 109.52 101.09 8.43 1.55e+00 4.16e-01 2.96e+01 angle pdb=" N ILE A 410 " pdb=" CA ILE A 410 " pdb=" C ILE A 410 " ideal model delta sigma weight residual 106.21 111.57 -5.36 1.07e+00 8.73e-01 2.51e+01 angle pdb=" N TYR J 51 " pdb=" CA TYR J 51 " pdb=" C TYR J 51 " ideal model delta sigma weight residual 109.52 101.84 7.68 1.55e+00 4.16e-01 2.45e+01 angle pdb=" C THR B 333 " pdb=" N ASN B 334 " pdb=" CA ASN B 334 " ideal model delta sigma weight residual 121.54 130.42 -8.88 1.91e+00 2.74e-01 2.16e+01 ... (remaining 37872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 14595 17.32 - 34.63: 1132 34.63 - 51.95: 237 51.95 - 69.27: 56 69.27 - 86.58: 24 Dihedral angle restraints: 16044 sinusoidal: 5827 harmonic: 10217 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -2.60 -83.40 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -4.42 -81.58 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -4.48 -81.52 1 1.00e+01 1.00e-02 8.18e+01 ... (remaining 16041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 4296 0.128 - 0.255: 115 0.255 - 0.383: 2 0.383 - 0.511: 0 0.511 - 0.638: 1 Chirality restraints: 4414 Sorted by residual: chirality pdb=" CB THR B 167 " pdb=" CA THR B 167 " pdb=" OG1 THR B 167 " pdb=" CG2 THR B 167 " both_signs ideal model delta sigma weight residual False 2.55 1.91 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CB ILE C 434 " pdb=" CA ILE C 434 " pdb=" CG1 ILE C 434 " pdb=" CG2 ILE C 434 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA CYS A 649 " pdb=" N CYS A 649 " pdb=" C CYS A 649 " pdb=" CB CYS A 649 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 4411 not shown) Planarity restraints: 4856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.065 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO C 373 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 372 " 0.063 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO B 373 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " 0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO C 330 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " 0.047 5.00e-02 4.00e+02 ... (remaining 4853 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 642 2.66 - 3.22: 26611 3.22 - 3.78: 41095 3.78 - 4.34: 54564 4.34 - 4.90: 90672 Nonbonded interactions: 213584 Sorted by model distance: nonbonded pdb=" O PRO C 85 " pdb=" OH TYR C 269 " model vdw 2.098 3.040 nonbonded pdb=" ND2 ASN A 394 " pdb=" OH TYR B 200 " model vdw 2.104 3.120 nonbonded pdb=" OG SER C 349 " pdb=" O ARG C 452 " model vdw 2.106 3.040 nonbonded pdb=" O ASN B 81 " pdb=" NE2 GLN B 239 " model vdw 2.125 3.120 nonbonded pdb=" O ASN C 978 " pdb=" OG SER C 982 " model vdw 2.125 3.040 ... (remaining 213579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 370 or (resid 371 through 372 and (name N or na \ me CA or name C or name O or name CB )) or resid 373 through 414 or (resid 415 a \ nd (name N or name CA or name C or name O or name CB )) or resid 416 through 417 \ or (resid 418 through 419 and (name N or name CA or name C or name O or name CB \ )) or resid 420 or (resid 421 and (name N or name CA or name C or name O or nam \ e CB )) or resid 422 through 426 or (resid 427 through 428 and (name N or name C \ A or name C or name O or name CB )) or resid 429 through 457 or (resid 458 and ( \ name N or name CA or name C or name O or name CB )) or resid 459 through 461 or \ (resid 462 and (name N or name CA or name C or name O or name CB )) or resid 463 \ through 473 or (resid 474 through 475 and (name N or name CA or name C or name \ O or name CB )) or resid 476 through 477 or (resid 478 and (name N or name CA or \ name C or name O or name CB )) or resid 479 through 486 or (resid 487 and (name \ N or name CA or name C or name O or name CB )) or resid 488 through 515 or (res \ id 516 and (name N or name CA or name C or name O or name CB )) or resid 517 thr \ ough 522 or (resid 523 and (name N or name CA or name C or name O or name CB )) \ or resid 524 through 1312)) selection = (chain 'B' and resid 27 through 1312) selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 13.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 27.820 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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: 0.020 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.008 0.139 27787 Z= 0.372 Angle : 0.985 12.618 37961 Z= 0.534 Chirality : 0.056 0.638 4414 Planarity : 0.005 0.101 4856 Dihedral : 13.341 86.582 9364 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.67 % Favored : 94.84 % Rotamer: Outliers : 1.54 % Allowed : 8.21 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.13), residues: 3472 helix: 0.26 (0.20), residues: 641 sheet: -0.86 (0.15), residues: 938 loop : -2.02 (0.12), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1000 TYR 0.039 0.003 TYR C 453 PHE 0.032 0.003 PHE A1089 TRP 0.050 0.004 TRP H 110 HIS 0.007 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00839 / 0.37 (27745) covalent geometry : angle 0.97245 / 0.53 (37877) SS BOND : bond 0.00759 / 0.53 ( 42) SS BOND : angle 3.42810 / 2.18 ( 84) hydrogen bonds : bond 0.21791 / 14.35 ( 1093) hydrogen bonds : angle 8.27244 / 5.78 ( 3018) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7564 (m-80) cc_final: 0.7329 (m-10) REVERT: A 169 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8591 (mm-30) REVERT: A 200 TYR cc_start: 0.9161 (m-80) cc_final: 0.8928 (m-80) REVERT: A 229 LEU cc_start: 0.9042 (mt) cc_final: 0.8833 (mt) REVERT: A 378 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8817 (mttt) REVERT: A 392 PHE cc_start: 0.8407 (m-80) cc_final: 0.8063 (m-10) REVERT: A 481 ASN cc_start: 0.9214 (m-40) cc_final: 0.8734 (p0) REVERT: A 516 GLU cc_start: 0.8254 (tt0) cc_final: 0.7889 (tm-30) REVERT: A 773 GLU cc_start: 0.7870 (tm-30) cc_final: 0.6950 (tm-30) REVERT: A 777 ASN cc_start: 0.8499 (m-40) cc_final: 0.7714 (m110) REVERT: A 780 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7815 (mt-10) REVERT: A 983 ARG cc_start: 0.9010 (ptm-80) cc_final: 0.8769 (ttp80) REVERT: B 223 LEU cc_start: 0.9001 (mp) cc_final: 0.8642 (mt) REVERT: B 353 TRP cc_start: 0.7214 (p-90) cc_final: 0.6193 (p-90) REVERT: B 365 TYR cc_start: 0.8298 (m-80) cc_final: 0.7767 (m-80) REVERT: B 823 PHE cc_start: 0.8651 (m-80) cc_final: 0.8281 (m-80) REVERT: B 964 LYS cc_start: 0.9375 (tptp) cc_final: 0.9027 (tppt) REVERT: B 1002 GLN cc_start: 0.8377 (tm-30) cc_final: 0.8137 (tm-30) REVERT: B 1005 GLN cc_start: 0.9345 (tp-100) cc_final: 0.8799 (tp-100) REVERT: C 360 ASN cc_start: 0.8967 (t0) cc_final: 0.8750 (p0) REVERT: C 779 GLN cc_start: 0.9237 (mm-40) cc_final: 0.9029 (tp40) REVERT: C 960 ASN cc_start: 0.9509 (t0) cc_final: 0.9106 (t0) REVERT: I 67 ARG cc_start: 0.7553 (ptt180) cc_final: 0.7146 (ptt180) REVERT: J 50 ILE cc_start: 0.9398 (mm) cc_final: 0.9119 (mm) outliers start: 43 outliers final: 18 residues processed: 255 average time/residue: 0.2105 time to fit residues: 82.7819 Evaluate side-chains 142 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN A 540 ASN A 657 ASN A 955 ASN ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN B 188 ASN B 409 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1134 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 354 ASN C 417 ASN C 505 HIS C 709 ASN C 762 GLN C 926 GLN C1088 HIS K 81 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.088422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.053951 restraints weight = 119580.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.055723 restraints weight = 54202.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.056864 restraints weight = 33494.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.057599 restraints weight = 24695.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.057960 restraints weight = 20740.490| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 27787 Z= 0.195 Angle : 0.678 9.446 37961 Z= 0.357 Chirality : 0.045 0.164 4414 Planarity : 0.005 0.055 4856 Dihedral : 5.478 58.531 3798 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.41 % Favored : 95.54 % Rotamer: Outliers : 1.43 % Allowed : 11.21 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.13), residues: 3472 helix: 1.30 (0.21), residues: 653 sheet: -0.41 (0.16), residues: 923 loop : -1.68 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 765 TYR 0.020 0.002 TYR B1067 PHE 0.022 0.002 PHE A 515 TRP 0.020 0.002 TRP B 353 HIS 0.005 0.001 HIS J 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (27745) covalent geometry : angle 0.67152 / 0.35 (37877) SS BOND : bond 0.00549 / 0.39 ( 42) SS BOND : angle 2.09660 / 1.32 ( 84) hydrogen bonds : bond 0.05453 / 3.68 ( 1093) hydrogen bonds : angle 6.50956 / 4.53 ( 3018) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.9264 (m-80) cc_final: 0.8981 (m-80) REVERT: A 298 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8716 (tm-30) REVERT: A 378 LYS cc_start: 0.9121 (mmtm) cc_final: 0.8632 (mmtm) REVERT: A 516 GLU cc_start: 0.8013 (tt0) cc_final: 0.7762 (tm-30) REVERT: A 725 GLU cc_start: 0.8482 (tt0) cc_final: 0.8112 (tt0) REVERT: A 773 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7255 (tm-30) REVERT: A 1002 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8628 (tm-30) REVERT: A 1029 MET cc_start: 0.9402 (tpp) cc_final: 0.8662 (tpp) REVERT: B 336 CYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7368 (m) REVERT: B 353 TRP cc_start: 0.6077 (p-90) cc_final: 0.5200 (p-90) REVERT: B 365 TYR cc_start: 0.8090 (m-80) cc_final: 0.7710 (m-80) REVERT: B 515 PHE cc_start: 0.8887 (p90) cc_final: 0.8562 (p90) REVERT: B 964 LYS cc_start: 0.9450 (tptp) cc_final: 0.9037 (tppt) REVERT: B 1005 GLN cc_start: 0.9445 (tp-100) cc_final: 0.8857 (tp-100) REVERT: B 1029 MET cc_start: 0.9481 (tpp) cc_final: 0.9260 (tpp) REVERT: B 1138 TYR cc_start: 0.8612 (m-80) cc_final: 0.8404 (m-10) REVERT: C 282 ASN cc_start: 0.9376 (OUTLIER) cc_final: 0.9099 (m-40) REVERT: C 754 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9309 (mt) REVERT: C 779 GLN cc_start: 0.9341 (mm-40) cc_final: 0.9075 (tp40) REVERT: C 960 ASN cc_start: 0.9546 (t0) cc_final: 0.9234 (m110) REVERT: C 1029 MET cc_start: 0.9526 (tpp) cc_final: 0.9325 (tpp) REVERT: I 100 VAL cc_start: 0.7978 (p) cc_final: 0.7762 (p) REVERT: J 50 ILE cc_start: 0.9172 (mm) cc_final: 0.8950 (mm) outliers start: 40 outliers final: 21 residues processed: 194 average time/residue: 0.1804 time to fit residues: 57.1554 Evaluate side-chains 145 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 59 TYR Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 166 optimal weight: 0.6980 chunk 263 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 299 optimal weight: 1.9990 chunk 137 optimal weight: 40.0000 chunk 234 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 978 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.088489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053620 restraints weight = 120799.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.055366 restraints weight = 56083.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.056530 restraints weight = 35088.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.057142 restraints weight = 26119.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.057519 restraints weight = 22122.622| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 27787 Z= 0.175 Angle : 0.617 8.179 37961 Z= 0.323 Chirality : 0.044 0.162 4414 Planarity : 0.004 0.052 4856 Dihedral : 5.199 58.942 3785 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.38 % Favored : 95.56 % Rotamer: Outliers : 2.61 % Allowed : 12.25 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3472 helix: 1.48 (0.21), residues: 651 sheet: -0.31 (0.16), residues: 940 loop : -1.39 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 112 TYR 0.019 0.001 TYR B1067 PHE 0.032 0.001 PHE A 375 TRP 0.015 0.001 TRP H 110 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (27745) covalent geometry : angle 0.61222 / 0.32 (37877) SS BOND : bond 0.00521 / 0.39 ( 42) SS BOND : angle 1.74794 / 1.13 ( 84) hydrogen bonds : bond 0.04945 / 3.33 ( 1093) hydrogen bonds : angle 6.07067 / 4.21 ( 3018) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 134 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.9247 (m-80) cc_final: 0.9007 (m-80) REVERT: A 298 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8747 (tm-30) REVERT: A 378 LYS cc_start: 0.9190 (mmtm) cc_final: 0.8695 (mmtm) REVERT: A 725 GLU cc_start: 0.8424 (tt0) cc_final: 0.8088 (tt0) REVERT: A 773 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 777 ASN cc_start: 0.7998 (m110) cc_final: 0.7751 (m-40) REVERT: A 1002 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8550 (tm-30) REVERT: A 1029 MET cc_start: 0.9407 (tpp) cc_final: 0.8588 (tpp) REVERT: B 336 CYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7301 (m) REVERT: B 365 TYR cc_start: 0.7982 (m-80) cc_final: 0.7659 (m-80) REVERT: B 515 PHE cc_start: 0.8894 (p90) cc_final: 0.8623 (p90) REVERT: B 712 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9203 (mm) REVERT: B 964 LYS cc_start: 0.9452 (tptp) cc_final: 0.9077 (tppt) REVERT: B 1005 GLN cc_start: 0.9415 (tp-100) cc_final: 0.8830 (tp-100) REVERT: C 282 ASN cc_start: 0.9492 (OUTLIER) cc_final: 0.9205 (m-40) REVERT: C 712 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8795 (mm) REVERT: C 754 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9248 (mt) REVERT: C 960 ASN cc_start: 0.9532 (t0) cc_final: 0.9219 (m110) REVERT: C 1010 GLN cc_start: 0.9272 (mm-40) cc_final: 0.9008 (mm-40) REVERT: I 67 ARG cc_start: 0.7673 (ptt180) cc_final: 0.7464 (ptt-90) REVERT: J 8 ARG cc_start: 0.8292 (mmp-170) cc_final: 0.8000 (mmp-170) REVERT: J 34 TYR cc_start: 0.8275 (m-80) cc_final: 0.7896 (m-80) outliers start: 73 outliers final: 41 residues processed: 199 average time/residue: 0.1698 time to fit residues: 55.9186 Evaluate side-chains 160 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 87 optimal weight: 5.9990 chunk 303 optimal weight: 4.9990 chunk 71 optimal weight: 0.0050 chunk 306 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 259 optimal weight: 1.9990 chunk 213 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 ASN A 955 ASN ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 417 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C1134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.086949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.052020 restraints weight = 121419.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.053715 restraints weight = 56229.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.054726 restraints weight = 35464.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.055531 restraints weight = 26691.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.055887 restraints weight = 22300.150| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 27787 Z= 0.254 Angle : 0.664 7.981 37961 Z= 0.346 Chirality : 0.044 0.156 4414 Planarity : 0.005 0.057 4856 Dihedral : 5.280 56.264 3785 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.75 % Favored : 95.22 % Rotamer: Outliers : 3.25 % Allowed : 13.54 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3472 helix: 1.20 (0.20), residues: 663 sheet: -0.35 (0.16), residues: 936 loop : -1.30 (0.13), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 815 TYR 0.022 0.002 TYR B1067 PHE 0.038 0.002 PHE A 371 TRP 0.020 0.002 TRP B 353 HIS 0.004 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.25 (27745) covalent geometry : angle 0.65970 / 0.34 (37877) SS BOND : bond 0.00535 / 0.39 ( 42) SS BOND : angle 1.79719 / 1.17 ( 84) hydrogen bonds : bond 0.05115 / 3.45 ( 1093) hydrogen bonds : angle 6.07660 / 4.22 ( 3018) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 121 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.9256 (m-80) cc_final: 0.9028 (m-80) REVERT: A 298 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8903 (tm-30) REVERT: A 378 LYS cc_start: 0.9216 (mmtm) cc_final: 0.8731 (mmtm) REVERT: A 773 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7591 (tm-30) REVERT: A 983 ARG cc_start: 0.9198 (tmm-80) cc_final: 0.8896 (ttp80) REVERT: A 1002 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8574 (tm-30) REVERT: A 1029 MET cc_start: 0.9437 (tpp) cc_final: 0.8608 (tpp) REVERT: B 336 CYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7301 (m) REVERT: B 365 TYR cc_start: 0.7860 (m-80) cc_final: 0.7541 (m-80) REVERT: B 515 PHE cc_start: 0.8928 (p90) cc_final: 0.8709 (p90) REVERT: B 712 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9216 (mm) REVERT: B 791 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8840 (p) REVERT: B 824 ASN cc_start: 0.9389 (m-40) cc_final: 0.9139 (m-40) REVERT: B 904 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.8052 (m-10) REVERT: B 960 ASN cc_start: 0.9601 (t0) cc_final: 0.9233 (t0) REVERT: B 964 LYS cc_start: 0.9514 (tptp) cc_final: 0.9176 (tppt) REVERT: B 1005 GLN cc_start: 0.9510 (tp-100) cc_final: 0.8888 (tp-100) REVERT: C 712 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8918 (mm) REVERT: C 754 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9226 (mt) REVERT: C 960 ASN cc_start: 0.9545 (t0) cc_final: 0.9137 (t0) REVERT: C 1010 GLN cc_start: 0.9298 (mm-40) cc_final: 0.9021 (mm-40) REVERT: I 67 ARG cc_start: 0.7753 (ptt180) cc_final: 0.7466 (ptt-90) REVERT: J 34 TYR cc_start: 0.8174 (m-80) cc_final: 0.7846 (m-80) REVERT: J 56 ARG cc_start: 0.8418 (mtm-85) cc_final: 0.8187 (mtm-85) outliers start: 91 outliers final: 54 residues processed: 204 average time/residue: 0.1721 time to fit residues: 58.4402 Evaluate side-chains 171 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 111 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 53 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 chunk 328 optimal weight: 0.0030 chunk 24 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 249 optimal weight: 50.0000 chunk 28 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 285 optimal weight: 0.9980 chunk 166 optimal weight: 0.5980 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 965 GLN B 239 GLN B 437 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 282 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 HIS J 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.089521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.055016 restraints weight = 115722.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.056715 restraints weight = 54722.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.057837 restraints weight = 34738.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.058585 restraints weight = 25987.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.058946 restraints weight = 21796.078| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27787 Z= 0.127 Angle : 0.565 9.086 37961 Z= 0.296 Chirality : 0.043 0.164 4414 Planarity : 0.004 0.055 4856 Dihedral : 4.938 55.467 3782 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.97 % Favored : 96.00 % Rotamer: Outliers : 2.96 % Allowed : 14.68 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.14), residues: 3472 helix: 1.66 (0.21), residues: 655 sheet: -0.12 (0.17), residues: 896 loop : -1.20 (0.13), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 19 TYR 0.017 0.001 TYR B1067 PHE 0.027 0.001 PHE A 371 TRP 0.022 0.001 TRP B 353 HIS 0.005 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (27745) covalent geometry : angle 0.56128 / 0.29 (37877) SS BOND : bond 0.00415 / 0.30 ( 42) SS BOND : angle 1.52742 / 0.97 ( 84) hydrogen bonds : bond 0.04373 / 2.92 ( 1093) hydrogen bonds : angle 5.61699 / 3.89 ( 3018) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 126 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8170 (t) REVERT: A 200 TYR cc_start: 0.9210 (m-80) cc_final: 0.8935 (m-80) REVERT: A 298 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8967 (tp30) REVERT: A 378 LYS cc_start: 0.9248 (mmtm) cc_final: 0.8744 (mmtm) REVERT: A 523 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8579 (t) REVERT: A 773 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7298 (tm-30) REVERT: A 777 ASN cc_start: 0.7900 (m110) cc_final: 0.7291 (m110) REVERT: A 983 ARG cc_start: 0.9236 (tmm-80) cc_final: 0.8982 (ttp80) REVERT: B 239 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7593 (tp40) REVERT: B 242 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8805 (mt) REVERT: B 333 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7782 (m) REVERT: B 336 CYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6982 (m) REVERT: B 365 TYR cc_start: 0.7745 (m-80) cc_final: 0.7446 (m-80) REVERT: B 515 PHE cc_start: 0.8961 (p90) cc_final: 0.8696 (p90) REVERT: B 712 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9179 (mm) REVERT: B 791 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8808 (p) REVERT: B 824 ASN cc_start: 0.9319 (m-40) cc_final: 0.9087 (m-40) REVERT: B 855 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6108 (m-80) REVERT: B 900 MET cc_start: 0.8844 (mtt) cc_final: 0.8580 (mtp) REVERT: B 904 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7815 (m-10) REVERT: B 960 ASN cc_start: 0.9549 (t0) cc_final: 0.9177 (t0) REVERT: B 964 LYS cc_start: 0.9462 (tptp) cc_final: 0.9083 (tppt) REVERT: B 1005 GLN cc_start: 0.9402 (tp-100) cc_final: 0.8761 (tp-100) REVERT: C 229 LEU cc_start: 0.8536 (tp) cc_final: 0.8293 (tp) REVERT: C 712 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8893 (mm) REVERT: C 754 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9232 (mt) REVERT: C 960 ASN cc_start: 0.9523 (t0) cc_final: 0.9220 (m110) REVERT: I 67 ARG cc_start: 0.7884 (ptt180) cc_final: 0.7554 (ptt-90) REVERT: J 34 TYR cc_start: 0.8241 (m-80) cc_final: 0.7891 (m-80) outliers start: 83 outliers final: 46 residues processed: 205 average time/residue: 0.1741 time to fit residues: 59.1632 Evaluate side-chains 176 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 118 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 239 optimal weight: 20.0000 chunk 205 optimal weight: 4.9990 chunk 227 optimal weight: 0.9980 chunk 338 optimal weight: 0.0030 chunk 216 optimal weight: 30.0000 chunk 308 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 288 optimal weight: 0.0170 chunk 321 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 overall best weight: 1.4030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.089499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.055157 restraints weight = 115265.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.056839 restraints weight = 54692.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.057962 restraints weight = 34628.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.058580 restraints weight = 25982.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.058800 restraints weight = 21884.816| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27787 Z= 0.131 Angle : 0.562 8.074 37961 Z= 0.294 Chirality : 0.043 0.171 4414 Planarity : 0.004 0.058 4856 Dihedral : 4.834 55.121 3782 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.18 % Allowed : 14.79 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3472 helix: 1.72 (0.21), residues: 655 sheet: -0.07 (0.17), residues: 908 loop : -1.11 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 19 TYR 0.018 0.001 TYR B1067 PHE 0.043 0.001 PHE A 392 TRP 0.017 0.001 TRP B 353 HIS 0.003 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (27745) covalent geometry : angle 0.55781 / 0.29 (37877) SS BOND : bond 0.00447 / 0.31 ( 42) SS BOND : angle 1.48572 / 0.96 ( 84) hydrogen bonds : bond 0.04279 / 2.86 ( 1093) hydrogen bonds : angle 5.51857 / 3.82 ( 3018) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 135 time to evaluate : 1.059 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 33 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8147 (t) REVERT: A 200 TYR cc_start: 0.9185 (m-80) cc_final: 0.8964 (m-80) REVERT: A 298 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8979 (tp30) REVERT: A 378 LYS cc_start: 0.9267 (mmtm) cc_final: 0.8756 (mmtm) REVERT: A 523 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8566 (t) REVERT: A 773 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7314 (tm-30) REVERT: A 777 ASN cc_start: 0.7856 (m110) cc_final: 0.7596 (m110) REVERT: A 983 ARG cc_start: 0.9241 (tmm-80) cc_final: 0.9027 (ttp80) REVERT: A 1029 MET cc_start: 0.9340 (tpp) cc_final: 0.8457 (tpp) REVERT: B 242 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8780 (mt) REVERT: B 333 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7788 (m) REVERT: B 336 CYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6807 (m) REVERT: B 365 TYR cc_start: 0.7743 (m-80) cc_final: 0.7440 (m-80) REVERT: B 515 PHE cc_start: 0.8988 (p90) cc_final: 0.8673 (p90) REVERT: B 712 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9178 (mm) REVERT: B 791 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8812 (p) REVERT: B 824 ASN cc_start: 0.9317 (m-40) cc_final: 0.9047 (m-40) REVERT: B 855 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6030 (m-80) REVERT: B 900 MET cc_start: 0.8858 (mtt) cc_final: 0.8600 (mtt) REVERT: B 904 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7771 (m-10) REVERT: B 960 ASN cc_start: 0.9543 (t0) cc_final: 0.9176 (t0) REVERT: B 964 LYS cc_start: 0.9457 (tptp) cc_final: 0.9051 (tppt) REVERT: C 712 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8888 (mm) REVERT: C 754 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9232 (mt) REVERT: C 960 ASN cc_start: 0.9512 (t0) cc_final: 0.9211 (m110) REVERT: J 34 TYR cc_start: 0.8267 (m-80) cc_final: 0.7886 (m-80) REVERT: H 34 MET cc_start: 0.4317 (mmt) cc_final: 0.3909 (tmm) outliers start: 89 outliers final: 61 residues processed: 217 average time/residue: 0.1731 time to fit residues: 62.5704 Evaluate side-chains 193 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 121 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 242 optimal weight: 8.9990 chunk 241 optimal weight: 20.0000 chunk 185 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 127 optimal weight: 0.0000 chunk 269 optimal weight: 4.9990 chunk 186 optimal weight: 0.2980 chunk 2 optimal weight: 9.9990 chunk 237 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.089744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.055368 restraints weight = 115875.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.057015 restraints weight = 55153.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.058185 restraints weight = 34710.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058834 restraints weight = 25934.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058834 restraints weight = 21791.878| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27787 Z= 0.121 Angle : 0.557 11.824 37961 Z= 0.288 Chirality : 0.043 0.162 4414 Planarity : 0.004 0.056 4856 Dihedral : 4.700 54.965 3782 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.89 % Allowed : 15.79 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3472 helix: 1.64 (0.21), residues: 670 sheet: -0.00 (0.17), residues: 907 loop : -0.99 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1019 TYR 0.018 0.001 TYR B1067 PHE 0.030 0.001 PHE A 392 TRP 0.014 0.001 TRP B 353 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (27745) covalent geometry : angle 0.55417 / 0.29 (37877) SS BOND : bond 0.00380 / 0.28 ( 42) SS BOND : angle 1.36241 / 0.88 ( 84) hydrogen bonds : bond 0.04094 / 2.72 ( 1093) hydrogen bonds : angle 5.37464 / 3.73 ( 3018) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 124 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8057 (t) REVERT: A 200 TYR cc_start: 0.9164 (m-80) cc_final: 0.8946 (m-80) REVERT: A 378 LYS cc_start: 0.9296 (mmtm) cc_final: 0.8793 (mmtm) REVERT: A 523 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8548 (t) REVERT: A 773 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7275 (tm-30) REVERT: A 777 ASN cc_start: 0.7734 (m110) cc_final: 0.7461 (m110) REVERT: A 983 ARG cc_start: 0.9263 (tmm-80) cc_final: 0.9025 (ttp80) REVERT: A 1002 GLN cc_start: 0.9190 (tp40) cc_final: 0.8844 (tp-100) REVERT: A 1029 MET cc_start: 0.9337 (tpp) cc_final: 0.8450 (tpp) REVERT: B 242 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8760 (mt) REVERT: B 336 CYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6687 (m) REVERT: B 365 TYR cc_start: 0.7747 (m-80) cc_final: 0.7425 (m-10) REVERT: B 515 PHE cc_start: 0.8959 (p90) cc_final: 0.8619 (p90) REVERT: B 712 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9125 (mm) REVERT: B 740 MET cc_start: 0.9342 (ttt) cc_final: 0.9110 (ttm) REVERT: B 791 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8836 (p) REVERT: B 824 ASN cc_start: 0.9300 (m-40) cc_final: 0.9031 (m-40) REVERT: B 855 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6064 (m-80) REVERT: B 869 MET cc_start: 0.8956 (mtm) cc_final: 0.8749 (ptp) REVERT: B 900 MET cc_start: 0.8833 (mtt) cc_final: 0.8529 (mtt) REVERT: B 904 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.7780 (m-10) REVERT: B 960 ASN cc_start: 0.9529 (t0) cc_final: 0.9167 (t0) REVERT: B 964 LYS cc_start: 0.9449 (tptp) cc_final: 0.9037 (tppt) REVERT: C 712 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8883 (mm) REVERT: C 754 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9225 (mt) REVERT: C 960 ASN cc_start: 0.9514 (t0) cc_final: 0.9212 (m110) REVERT: I 67 ARG cc_start: 0.7925 (ptt180) cc_final: 0.7616 (ptt-90) REVERT: I 107 PHE cc_start: 0.8363 (t80) cc_final: 0.8131 (t80) REVERT: J 34 TYR cc_start: 0.8310 (m-80) cc_final: 0.7912 (m-80) REVERT: H 34 MET cc_start: 0.4142 (mmt) cc_final: 0.3722 (tmm) outliers start: 81 outliers final: 58 residues processed: 198 average time/residue: 0.1534 time to fit residues: 50.8824 Evaluate side-chains 184 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 116 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 62 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 201 optimal weight: 0.5980 chunk 216 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 310 optimal weight: 20.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.088936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054592 restraints weight = 117192.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.056257 restraints weight = 56198.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.057371 restraints weight = 35615.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.057805 restraints weight = 26806.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.058273 restraints weight = 23200.090| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 27787 Z= 0.165 Angle : 0.589 13.421 37961 Z= 0.303 Chirality : 0.043 0.169 4414 Planarity : 0.004 0.059 4856 Dihedral : 4.751 56.126 3781 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.82 % Allowed : 16.18 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3472 helix: 1.67 (0.21), residues: 664 sheet: -0.04 (0.16), residues: 914 loop : -0.97 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 403 TYR 0.020 0.001 TYR B1067 PHE 0.024 0.001 PHE A 392 TRP 0.013 0.001 TRP B 353 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (27745) covalent geometry : angle 0.58478 / 0.30 (37877) SS BOND : bond 0.00425 / 0.31 ( 42) SS BOND : angle 1.53266 / 0.99 ( 84) hydrogen bonds : bond 0.04291 / 2.86 ( 1093) hydrogen bonds : angle 5.46920 / 3.79 ( 3018) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 124 time to evaluate : 0.969 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 33 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8073 (t) REVERT: A 200 TYR cc_start: 0.9175 (m-80) cc_final: 0.8938 (m-80) REVERT: A 378 LYS cc_start: 0.9312 (mmtm) cc_final: 0.8835 (mmtm) REVERT: A 523 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8562 (t) REVERT: A 773 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 983 ARG cc_start: 0.9247 (tmm-80) cc_final: 0.9020 (ttp80) REVERT: A 1002 GLN cc_start: 0.9216 (tp40) cc_final: 0.8839 (tp-100) REVERT: A 1029 MET cc_start: 0.9383 (tpp) cc_final: 0.8593 (tpp) REVERT: B 242 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8728 (mt) REVERT: B 336 CYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6700 (m) REVERT: B 353 TRP cc_start: 0.6610 (p-90) cc_final: 0.6110 (p-90) REVERT: B 365 TYR cc_start: 0.7676 (m-80) cc_final: 0.7332 (m-10) REVERT: B 515 PHE cc_start: 0.8957 (p90) cc_final: 0.8620 (p90) REVERT: B 517 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8780 (mm) REVERT: B 712 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9147 (mm) REVERT: B 791 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8859 (p) REVERT: B 824 ASN cc_start: 0.9307 (m-40) cc_final: 0.9066 (m-40) REVERT: B 869 MET cc_start: 0.9007 (mtm) cc_final: 0.8733 (ptp) REVERT: B 904 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7899 (m-10) REVERT: B 960 ASN cc_start: 0.9531 (t0) cc_final: 0.9164 (t0) REVERT: B 964 LYS cc_start: 0.9473 (tptp) cc_final: 0.9054 (tppt) REVERT: C 712 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8923 (mm) REVERT: C 754 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9215 (mt) REVERT: C 904 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.8324 (m-10) REVERT: C 960 ASN cc_start: 0.9524 (t0) cc_final: 0.9235 (m110) REVERT: I 107 PHE cc_start: 0.8348 (t80) cc_final: 0.8030 (t80) REVERT: J 34 TYR cc_start: 0.8280 (m-80) cc_final: 0.8040 (m-80) REVERT: H 34 MET cc_start: 0.4149 (mmt) cc_final: 0.3698 (tmm) outliers start: 79 outliers final: 58 residues processed: 196 average time/residue: 0.1639 time to fit residues: 53.7177 Evaluate side-chains 187 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 118 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 125 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 212 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.088798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.054506 restraints weight = 116626.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.056128 restraints weight = 55743.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.057224 restraints weight = 35862.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.057849 restraints weight = 27143.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058359 restraints weight = 22915.517| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27787 Z= 0.183 Angle : 0.599 13.835 37961 Z= 0.311 Chirality : 0.043 0.165 4414 Planarity : 0.004 0.056 4856 Dihedral : 4.775 55.590 3779 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.79 % Allowed : 16.57 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3472 helix: 1.54 (0.21), residues: 676 sheet: -0.10 (0.16), residues: 921 loop : -0.95 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1019 TYR 0.021 0.001 TYR B1067 PHE 0.022 0.001 PHE A 392 TRP 0.013 0.001 TRP B 353 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (27745) covalent geometry : angle 0.59522 / 0.31 (37877) SS BOND : bond 0.00457 / 0.33 ( 42) SS BOND : angle 1.57061 / 1.02 ( 84) hydrogen bonds : bond 0.04404 / 2.95 ( 1093) hydrogen bonds : angle 5.52458 / 3.82 ( 3018) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 121 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8097 (t) REVERT: A 200 TYR cc_start: 0.9188 (m-80) cc_final: 0.8923 (m-80) REVERT: A 378 LYS cc_start: 0.9331 (mmtm) cc_final: 0.8861 (mmtm) REVERT: A 983 ARG cc_start: 0.9206 (tmm-80) cc_final: 0.8997 (ttp80) REVERT: A 1002 GLN cc_start: 0.9220 (tp40) cc_final: 0.8838 (tp-100) REVERT: A 1029 MET cc_start: 0.9378 (tpp) cc_final: 0.8510 (tpp) REVERT: B 81 ASN cc_start: 0.6532 (OUTLIER) cc_final: 0.5831 (t0) REVERT: B 242 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8697 (mt) REVERT: B 298 GLU cc_start: 0.9343 (tt0) cc_final: 0.9011 (mt-10) REVERT: B 336 CYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6774 (m) REVERT: B 353 TRP cc_start: 0.6679 (p-90) cc_final: 0.6213 (p-90) REVERT: B 365 TYR cc_start: 0.7606 (m-80) cc_final: 0.7337 (m-80) REVERT: B 515 PHE cc_start: 0.8968 (p90) cc_final: 0.8636 (p90) REVERT: B 712 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9126 (mm) REVERT: B 824 ASN cc_start: 0.9316 (m-40) cc_final: 0.9056 (m-40) REVERT: B 904 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.7936 (m-10) REVERT: B 960 ASN cc_start: 0.9531 (t0) cc_final: 0.9161 (t0) REVERT: B 964 LYS cc_start: 0.9482 (tptp) cc_final: 0.9102 (tppt) REVERT: C 712 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.8916 (mm) REVERT: C 754 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9207 (mt) REVERT: C 904 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8315 (m-10) REVERT: C 960 ASN cc_start: 0.9519 (t0) cc_final: 0.9235 (m110) REVERT: I 107 PHE cc_start: 0.8376 (t80) cc_final: 0.8061 (t80) REVERT: J 34 TYR cc_start: 0.8268 (m-80) cc_final: 0.7964 (m-80) REVERT: H 34 MET cc_start: 0.4101 (mmt) cc_final: 0.3639 (tmm) outliers start: 78 outliers final: 61 residues processed: 193 average time/residue: 0.1543 time to fit residues: 49.8835 Evaluate side-chains 189 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 119 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain K residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 249 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 chunk 191 optimal weight: 0.7980 chunk 237 optimal weight: 10.0000 chunk 273 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 chunk 308 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 239 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN H 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.089006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.054787 restraints weight = 115949.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.056427 restraints weight = 55516.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.057526 restraints weight = 35557.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.058096 restraints weight = 26930.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.058096 restraints weight = 22794.807| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27787 Z= 0.155 Angle : 0.586 14.803 37961 Z= 0.305 Chirality : 0.043 0.159 4414 Planarity : 0.004 0.060 4856 Dihedral : 4.730 55.940 3779 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.57 % Allowed : 17.18 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3472 helix: 1.51 (0.21), residues: 683 sheet: -0.07 (0.17), residues: 918 loop : -0.91 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1019 TYR 0.026 0.001 TYR A1138 PHE 0.022 0.001 PHE B 238 TRP 0.012 0.001 TRP B 353 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (27745) covalent geometry : angle 0.58255 / 0.30 (37877) SS BOND : bond 0.00434 / 0.31 ( 42) SS BOND : angle 1.49975 / 0.98 ( 84) hydrogen bonds : bond 0.04275 / 2.85 ( 1093) hydrogen bonds : angle 5.45940 / 3.78 ( 3018) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 121 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8063 (t) REVERT: A 200 TYR cc_start: 0.9194 (m-80) cc_final: 0.8924 (m-80) REVERT: A 378 LYS cc_start: 0.9333 (mmtm) cc_final: 0.8873 (mmtm) REVERT: A 983 ARG cc_start: 0.9244 (tmm-80) cc_final: 0.9023 (ttp80) REVERT: A 1002 GLN cc_start: 0.9212 (tp40) cc_final: 0.8824 (tp-100) REVERT: A 1029 MET cc_start: 0.9348 (tpp) cc_final: 0.8452 (tpp) REVERT: B 242 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8657 (mt) REVERT: B 298 GLU cc_start: 0.9345 (tt0) cc_final: 0.9010 (mt-10) REVERT: B 336 CYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6792 (m) REVERT: B 353 TRP cc_start: 0.6686 (p-90) cc_final: 0.6227 (p-90) REVERT: B 365 TYR cc_start: 0.7577 (m-80) cc_final: 0.7305 (m-80) REVERT: B 515 PHE cc_start: 0.8957 (p90) cc_final: 0.8615 (p90) REVERT: B 712 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9117 (mm) REVERT: B 824 ASN cc_start: 0.9312 (m-40) cc_final: 0.9055 (m-40) REVERT: B 904 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7909 (m-10) REVERT: B 960 ASN cc_start: 0.9528 (t0) cc_final: 0.9160 (t0) REVERT: B 964 LYS cc_start: 0.9471 (tptp) cc_final: 0.9072 (tppt) REVERT: C 712 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8922 (mm) REVERT: C 754 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9198 (mt) REVERT: C 904 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8278 (m-10) REVERT: C 960 ASN cc_start: 0.9517 (t0) cc_final: 0.9239 (m110) REVERT: I 107 PHE cc_start: 0.8431 (t80) cc_final: 0.8110 (t80) REVERT: J 34 TYR cc_start: 0.8306 (m-80) cc_final: 0.7978 (m-80) REVERT: H 34 MET cc_start: 0.4044 (mmt) cc_final: 0.3588 (tmm) outliers start: 72 outliers final: 59 residues processed: 187 average time/residue: 0.1733 time to fit residues: 53.9673 Evaluate side-chains 186 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 119 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain K residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 296 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 148 optimal weight: 30.0000 chunk 26 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 210 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 276 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN A 506 GLN B 81 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.088404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.054118 restraints weight = 118066.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.055882 restraints weight = 54557.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.057048 restraints weight = 33971.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.057479 restraints weight = 25207.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.057931 restraints weight = 21788.370| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 27787 Z= 0.108 Angle : 0.563 15.479 37961 Z= 0.292 Chirality : 0.043 0.403 4414 Planarity : 0.004 0.056 4856 Dihedral : 4.536 55.113 3779 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.36 % Allowed : 17.14 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3472 helix: 1.64 (0.21), residues: 684 sheet: 0.06 (0.17), residues: 919 loop : -0.84 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1019 TYR 0.025 0.001 TYR J 34 PHE 0.022 0.001 PHE A 168 TRP 0.013 0.001 TRP B 436 HIS 0.005 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (27745) covalent geometry : angle 0.56019 / 0.29 (37877) SS BOND : bond 0.00358 / 0.26 ( 42) SS BOND : angle 1.24823 / 0.82 ( 84) hydrogen bonds : bond 0.03882 / 2.57 ( 1093) hydrogen bonds : angle 5.24039 / 3.61 ( 3018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5621.55 seconds wall clock time: 97 minutes 46.89 seconds (5866.89 seconds total)