Starting phenix.real_space_refine on Mon Jul 6 14:29:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ddx_27345/07_2026/8ddx_27345.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ddx_27345/07_2026/8ddx_27345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ddx_27345/07_2026/8ddx_27345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ddx_27345/07_2026/8ddx_27345.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ddx_27345/07_2026/8ddx_27345.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ddx_27345/07_2026/8ddx_27345.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ddx_27345/07_2026/8ddx_27345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ddx_27345/07_2026/8ddx_27345.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 259 5.16 5 Na 1 4.78 5 C 22948 2.51 5 N 5956 2.21 5 O 6320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 35500 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 8030 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 992, 8030 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 41, 'TRANS': 950} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "I" Number of atoms: 2598 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} bond proxies already assigned to first conformer: 2631 Chain: "J" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 484 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 171 Unusual residues: {' NA': 1, '3PH': 1, '9Z9': 2, 'PIO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'3PH': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N APHE A 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE A 913 " occ=0.47 residue: pdb=" N AMET A1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET A1011 " occ=0.57 residue: pdb=" N APHE B 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE B 913 " occ=0.47 residue: pdb=" N AMET B1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET B1011 " occ=0.57 residue: pdb=" N APHE C 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE C 913 " occ=0.47 residue: pdb=" N AMET C1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET C1011 " occ=0.57 residue: pdb=" N APHE D 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE D 913 " occ=0.47 residue: pdb=" N AMET D1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET D1011 " occ=0.57 Time building chain proxies: 7.65, per 1000 atoms: 0.22 Number of scatterers: 35500 At special positions: 0 Unit cell: (177.12, 163.08, 167.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 259 16.00 P 16 15.00 Na 1 11.00 O 6320 8.00 N 5956 7.00 C 22948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.92 Conformation dependent library (CDL) restraints added in 1.6 seconds 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8224 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 17 sheets defined 60.3% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 165 through 175 Processing helix chain 'A' and resid 201 through 216 removed outlier: 3.835A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.724A pdb=" N SER A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.876A pdb=" N LYS A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 413 through 423 removed outlier: 4.109A pdb=" N LYS A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 450 removed outlier: 3.501A pdb=" N LEU A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'A' and resid 468 through 475 Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 527 Processing helix chain 'A' and resid 536 through 544 Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.845A pdb=" N GLY A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 577 Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.603A pdb=" N ASN A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 648 removed outlier: 4.394A pdb=" N GLU A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 4.007A pdb=" N GLN A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 685 Processing helix chain 'A' and resid 690 through 717 Processing helix chain 'A' and resid 717 through 725 removed outlier: 3.755A pdb=" N ALA A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 725 " --> pdb=" O ALA A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 733 removed outlier: 3.915A pdb=" N SER A 733 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 746 through 751 removed outlier: 3.616A pdb=" N ILE A 750 " --> pdb=" O HIS A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 765 Processing helix chain 'A' and resid 774 through 783 Processing helix chain 'A' and resid 784 through 788 removed outlier: 3.873A pdb=" N LEU A 788 " --> pdb=" O PRO A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 869 removed outlier: 3.858A pdb=" N ASN A 869 " --> pdb=" O TYR A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 895 Processing helix chain 'A' and resid 902 through 925 Processing helix chain 'A' and resid 930 through 940 removed outlier: 3.884A pdb=" N LYS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 962 removed outlier: 3.662A pdb=" N VAL A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 985 removed outlier: 4.198A pdb=" N ASP A 970 " --> pdb=" O PRO A 966 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 972 " --> pdb=" O ARG A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 991 removed outlier: 4.157A pdb=" N ILE A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1033 removed outlier: 3.702A pdb=" N LYS A1005 " --> pdb=" O MET A1001 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE A1013 " --> pdb=" O ASP A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1046 Processing helix chain 'A' and resid 1047 through 1054 removed outlier: 3.960A pdb=" N ILE A1054 " --> pdb=" O PRO A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1105 removed outlier: 4.274A pdb=" N ALA A1093 " --> pdb=" O TRP A1089 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A1097 " --> pdb=" O ALA A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1118 through 1143 removed outlier: 4.490A pdb=" N TYR A1134 " --> pdb=" O LYS A1130 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A1143 " --> pdb=" O THR A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1164 removed outlier: 3.638A pdb=" N SER A1154 " --> pdb=" O LEU A1150 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET A1158 " --> pdb=" O SER A1154 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A1159 " --> pdb=" O HIS A1155 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A1160 " --> pdb=" O MET A1156 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A1163 " --> pdb=" O ILE A1159 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS A1164 " --> pdb=" O PHE A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1214 removed outlier: 3.551A pdb=" N SER A1214 " --> pdb=" O ASP A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1240 Processing helix chain 'B' and resid 165 through 175 Processing helix chain 'B' and resid 200 through 216 removed outlier: 3.850A pdb=" N VAL B 204 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 241 Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 343 through 354 removed outlier: 4.254A pdb=" N SER B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.520A pdb=" N LYS B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 439 through 452 removed outlier: 3.559A pdb=" N ALA B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 Processing helix chain 'B' and resid 468 through 475 removed outlier: 4.007A pdb=" N ALA B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 498 Processing helix chain 'B' and resid 500 through 509 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 527 Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.567A pdb=" N LYS B 545 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.658A pdb=" N GLY B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 577 removed outlier: 3.526A pdb=" N THR B 577 " --> pdb=" O CYS B 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 574 through 577' Processing helix chain 'B' and resid 578 through 586 Processing helix chain 'B' and resid 636 through 648 removed outlier: 4.555A pdb=" N GLU B 640 " --> pdb=" O PHE B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 removed outlier: 4.169A pdb=" N GLN B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 685 Processing helix chain 'B' and resid 690 through 717 Processing helix chain 'B' and resid 717 through 725 Processing helix chain 'B' and resid 736 through 744 Processing helix chain 'B' and resid 746 through 751 removed outlier: 3.560A pdb=" N ILE B 750 " --> pdb=" O HIS B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 765 removed outlier: 3.509A pdb=" N GLY B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 783 Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.678A pdb=" N LEU B 788 " --> pdb=" O PRO B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 869 removed outlier: 3.511A pdb=" N ASN B 869 " --> pdb=" O TYR B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 895 removed outlier: 3.533A pdb=" N VAL B 893 " --> pdb=" O PHE B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 925 Processing helix chain 'B' and resid 930 through 939 removed outlier: 4.063A pdb=" N VAL B 935 " --> pdb=" O LEU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.725A pdb=" N LEU B 948 " --> pdb=" O ASN B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 985 removed outlier: 4.262A pdb=" N ILE B 980 " --> pdb=" O CYS B 976 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR B 981 " --> pdb=" O VAL B 977 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 991 removed outlier: 4.061A pdb=" N ILE B 989 " --> pdb=" O ARG B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1033 removed outlier: 4.132A pdb=" N ILE B1008 " --> pdb=" O GLY B1004 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N TYR B1012 " --> pdb=" O ILE B1008 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N PHE B1013 " --> pdb=" O ASP B1009 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B1015 " --> pdb=" O AMET B1011 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B1017 " --> pdb=" O PHE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1046 Processing helix chain 'B' and resid 1047 through 1054 removed outlier: 3.783A pdb=" N ILE B1054 " --> pdb=" O PRO B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1089 No H-bonds generated for 'chain 'B' and resid 1087 through 1089' Processing helix chain 'B' and resid 1090 through 1105 Processing helix chain 'B' and resid 1105 through 1117 Processing helix chain 'B' and resid 1118 through 1142 removed outlier: 4.656A pdb=" N TYR B1134 " --> pdb=" O LYS B1130 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1147 through 1149 No H-bonds generated for 'chain 'B' and resid 1147 through 1149' Processing helix chain 'B' and resid 1150 through 1164 removed outlier: 4.432A pdb=" N SER B1154 " --> pdb=" O LEU B1150 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B1163 " --> pdb=" O ILE B1159 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1214 Processing helix chain 'B' and resid 1215 through 1240 removed outlier: 3.819A pdb=" N ARG B1219 " --> pdb=" O SER B1215 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B1240 " --> pdb=" O GLU B1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 176 removed outlier: 3.596A pdb=" N LEU C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 216 removed outlier: 3.805A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.752A pdb=" N HIS C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 259 No H-bonds generated for 'chain 'C' and resid 257 through 259' Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 308 through 322 Processing helix chain 'C' and resid 342 through 353 removed outlier: 4.173A pdb=" N ILE C 346 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 347 " --> pdb=" O PRO C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.708A pdb=" N LYS C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 439 through 453 removed outlier: 3.554A pdb=" N ASN C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 466 Processing helix chain 'C' and resid 468 through 475 removed outlier: 4.337A pdb=" N ALA C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 499 removed outlier: 3.663A pdb=" N GLN C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 510 Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 536 through 546 Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.532A pdb=" N ILE C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 569 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 636 through 648 removed outlier: 4.184A pdb=" N GLU C 640 " --> pdb=" O PHE C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 3.907A pdb=" N GLN C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 685 Processing helix chain 'C' and resid 690 through 717 Processing helix chain 'C' and resid 718 through 725 removed outlier: 3.761A pdb=" N LEU C 725 " --> pdb=" O ALA C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 744 Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.609A pdb=" N ILE C 750 " --> pdb=" O HIS C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 764 Processing helix chain 'C' and resid 772 through 783 removed outlier: 3.712A pdb=" N LYS C 776 " --> pdb=" O ASN C 772 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 778 " --> pdb=" O GLY C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 789 removed outlier: 3.841A pdb=" N LEU C 788 " --> pdb=" O PRO C 784 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER C 789 " --> pdb=" O PRO C 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 784 through 789' Processing helix chain 'C' and resid 862 through 869 Processing helix chain 'C' and resid 870 through 895 Processing helix chain 'C' and resid 902 through 925 Processing helix chain 'C' and resid 930 through 939 removed outlier: 3.783A pdb=" N VAL C 935 " --> pdb=" O LEU C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 962 removed outlier: 3.818A pdb=" N VAL C 945 " --> pdb=" O GLU C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 991 removed outlier: 4.060A pdb=" N LEU C 986 " --> pdb=" O TRP C 982 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU C 987 " --> pdb=" O TYR C 983 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP C 988 " --> pdb=" O ILE C 984 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE C 989 " --> pdb=" O ARG C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1033 removed outlier: 4.047A pdb=" N ILE C1008 " --> pdb=" O GLY C1004 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE C1015 " --> pdb=" O AMET C1011 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE C1016 " --> pdb=" O TYR C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1054 removed outlier: 3.511A pdb=" N ASN C1045 " --> pdb=" O LYS C1041 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE C1046 " --> pdb=" O LEU C1042 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE C1047 " --> pdb=" O ALA C1043 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET C1049 " --> pdb=" O ASN C1045 " (cutoff:3.500A) Proline residue: C1050 - end of helix removed outlier: 3.821A pdb=" N ILE C1054 " --> pdb=" O PRO C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1105 removed outlier: 4.393A pdb=" N ALA C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1105 through 1117 Processing helix chain 'C' and resid 1118 through 1143 removed outlier: 4.794A pdb=" N TYR C1134 " --> pdb=" O LYS C1130 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLN C1135 " --> pdb=" O PHE C1131 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG C1143 " --> pdb=" O THR C1139 " (cutoff:3.500A) Processing helix chain 'C' and resid 1147 through 1149 No H-bonds generated for 'chain 'C' and resid 1147 through 1149' Processing helix chain 'C' and resid 1150 through 1164 removed outlier: 4.291A pdb=" N SER C1154 " --> pdb=" O LEU C1150 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL C1163 " --> pdb=" O ILE C1159 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS C1164 " --> pdb=" O PHE C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1213 Processing helix chain 'C' and resid 1215 through 1240 Processing helix chain 'D' and resid 165 through 175 removed outlier: 3.604A pdb=" N LEU D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 216 removed outlier: 3.714A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.616A pdb=" N HIS D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.920A pdb=" N LYS D 283 " --> pdb=" O PRO D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 320 Processing helix chain 'D' and resid 344 through 355 Processing helix chain 'D' and resid 369 through 379 removed outlier: 4.045A pdb=" N LYS D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 402 removed outlier: 3.646A pdb=" N LYS D 401 " --> pdb=" O THR D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 439 through 450 Processing helix chain 'D' and resid 451 through 453 No H-bonds generated for 'chain 'D' and resid 451 through 453' Processing helix chain 'D' and resid 455 through 467 Processing helix chain 'D' and resid 468 through 475 removed outlier: 3.536A pdb=" N ALA D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 498 removed outlier: 3.873A pdb=" N GLN D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 509 Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 527 Processing helix chain 'D' and resid 536 through 544 Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.548A pdb=" N GLY D 569 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 587 removed outlier: 3.830A pdb=" N ASN D 587 " --> pdb=" O THR D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 601 removed outlier: 3.883A pdb=" N LEU D 599 " --> pdb=" O LYS D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 648 removed outlier: 4.071A pdb=" N GLU D 640 " --> pdb=" O PHE D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 659 removed outlier: 4.070A pdb=" N GLN D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 685 Processing helix chain 'D' and resid 690 through 717 Processing helix chain 'D' and resid 717 through 727 removed outlier: 3.515A pdb=" N ALA D 721 " --> pdb=" O ASP D 717 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR D 726 " --> pdb=" O MET D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 744 Processing helix chain 'D' and resid 746 through 751 removed outlier: 3.501A pdb=" N ILE D 750 " --> pdb=" O HIS D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 765 Processing helix chain 'D' and resid 774 through 783 removed outlier: 3.799A pdb=" N LEU D 782 " --> pdb=" O ILE D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 789 removed outlier: 3.925A pdb=" N LEU D 788 " --> pdb=" O PRO D 785 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D 789 " --> pdb=" O SER D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 868 Processing helix chain 'D' and resid 870 through 895 removed outlier: 3.505A pdb=" N LYS D 874 " --> pdb=" O ALA D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 926 removed outlier: 3.505A pdb=" N SER D 926 " --> pdb=" O GLU D 922 " (cutoff:3.500A) Processing helix chain 'D' and resid 930 through 939 removed outlier: 3.508A pdb=" N VAL D 935 " --> pdb=" O LEU D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 941 through 962 removed outlier: 3.783A pdb=" N VAL D 945 " --> pdb=" O GLU D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 964 through 985 removed outlier: 4.183A pdb=" N ILE D 980 " --> pdb=" O CYS D 976 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR D 981 " --> pdb=" O VAL D 977 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP D 982 " --> pdb=" O ASN D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 991 removed outlier: 3.826A pdb=" N ILE D 989 " --> pdb=" O ARG D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 996 through 1033 removed outlier: 3.992A pdb=" N ILE D1008 " --> pdb=" O GLY D1004 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TYR D1012 " --> pdb=" O ILE D1008 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE D1013 " --> pdb=" O ASP D1009 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1054 removed outlier: 3.577A pdb=" N ASN D1045 " --> pdb=" O LYS D1041 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE D1046 " --> pdb=" O LEU D1042 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE D1047 " --> pdb=" O ALA D1043 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N MET D1049 " --> pdb=" O ASN D1045 " (cutoff:3.500A) Proline residue: D1050 - end of helix removed outlier: 3.901A pdb=" N ILE D1054 " --> pdb=" O PRO D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1090 through 1116 removed outlier: 3.581A pdb=" N CYS D1097 " --> pdb=" O ALA D1093 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU D1106 " --> pdb=" O ALA D1102 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL D1107 " --> pdb=" O ASN D1103 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN D1108 " --> pdb=" O ILE D1104 " (cutoff:3.500A) Processing helix chain 'D' and resid 1117 through 1143 removed outlier: 3.651A pdb=" N VAL D1121 " --> pdb=" O THR D1117 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TYR D1134 " --> pdb=" O LYS D1130 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN D1135 " --> pdb=" O PHE D1131 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG D1143 " --> pdb=" O THR D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1164 removed outlier: 3.504A pdb=" N PHE D1160 " --> pdb=" O MET D1156 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D1163 " --> pdb=" O ILE D1159 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS D1164 " --> pdb=" O PHE D1160 " (cutoff:3.500A) Processing helix chain 'D' and resid 1186 through 1214 Processing helix chain 'D' and resid 1215 through 1240 Processing helix chain 'I' and resid 10 through 24 removed outlier: 3.732A pdb=" N LEU I 14 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE I 18 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS I 23 " --> pdb=" O ARG I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 37 removed outlier: 3.980A pdb=" N ASN I 36 " --> pdb=" O ILE I 33 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE I 37 " --> pdb=" O THR I 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 33 through 37' Processing helix chain 'J' and resid 9 through 23 removed outlier: 3.660A pdb=" N LYS J 14 " --> pdb=" O ALA J 10 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU J 15 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN J 18 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA J 23 " --> pdb=" O LEU J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 34 Processing helix chain 'J' and resid 36 through 46 removed outlier: 3.745A pdb=" N TYR J 40 " --> pdb=" O ASP J 36 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS J 46 " --> pdb=" O GLU J 42 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 removed outlier: 3.572A pdb=" N UNK E 10 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 271 through 275 removed outlier: 6.806A pdb=" N THR A 143 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N TYR A 274 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU A 145 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N PHE A 294 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N MET A 156 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU A 296 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL A 158 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ASP A 298 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL A 160 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA A 218 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 251 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE A 220 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 253 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N THR A 222 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU A 185 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU A 337 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N SER A 187 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 361 " --> pdb=" O THR A 428 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N PHE A 430 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 363 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 270 through 273 removed outlier: 7.068A pdb=" N PHE B 141 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG B 272 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR B 143 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR B 250 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE B 295 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY B 252 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA B 297 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 254 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE B 220 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 253 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR B 222 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 186 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 185 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU B 337 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER B 187 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL B 361 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE B 430 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 363 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AA5, first strand: chain 'C' and resid 272 through 275 removed outlier: 8.157A pdb=" N ARG C 272 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N THR C 143 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N TYR C 274 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU C 145 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 158 " --> pdb=" O PHE C 294 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS C 293 " --> pdb=" O THR C 250 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ALA C 218 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE C 251 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE C 220 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE C 253 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR C 222 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU C 184 " --> pdb=" O TRP C 219 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N PHE C 221 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE C 186 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU C 185 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU C 337 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N SER C 187 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL C 361 " --> pdb=" O THR C 428 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N PHE C 430 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL C 363 " --> pdb=" O PHE C 430 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 133 through 134 removed outlier: 3.505A pdb=" N GLN D 134 " --> pdb=" O UNK H 10 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N UNK H 10 " --> pdb=" O GLN D 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 251 through 255 removed outlier: 6.818A pdb=" N THR D 143 " --> pdb=" O ARG D 272 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N TYR D 274 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLU D 145 " --> pdb=" O TYR D 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 219 through 221 removed outlier: 6.142A pdb=" N LEU D 185 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU D 337 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER D 187 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL D 339 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N HIS D 189 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 46 through 51 removed outlier: 4.123A pdb=" N ARG I 46 " --> pdb=" O ASN I 340 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE I 338 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR I 50 " --> pdb=" O LEU I 336 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU I 336 " --> pdb=" O THR I 50 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS I 337 " --> pdb=" O THR I 329 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 58 through 62 removed outlier: 6.773A pdb=" N ALA I 73 " --> pdb=" O TYR I 59 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N MET I 61 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL I 71 " --> pdb=" O MET I 61 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 78 through 82 removed outlier: 4.538A pdb=" N HIS I 91 " --> pdb=" O ILE I 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 100 through 103 removed outlier: 6.114A pdb=" N GLY I 115 " --> pdb=" O MET I 101 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS I 103 " --> pdb=" O ALA I 113 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ALA I 113 " --> pdb=" O CYS I 103 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER I 122 " --> pdb=" O CYS I 114 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLY I 116 " --> pdb=" O ILE I 120 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE I 120 " --> pdb=" O GLY I 116 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N CYS I 121 " --> pdb=" O GLU I 138 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU I 138 " --> pdb=" O CYS I 121 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE I 123 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG I 134 " --> pdb=" O ASN I 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 146 through 151 removed outlier: 3.720A pdb=" N ILE I 157 " --> pdb=" O TRP I 169 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR I 159 " --> pdb=" O ALA I 167 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA I 167 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER I 161 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR I 165 " --> pdb=" O SER I 161 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR I 178 " --> pdb=" O LEU I 168 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASP I 170 " --> pdb=" O GLN I 176 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLN I 176 " --> pdb=" O ASP I 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 198 through 199 Processing sheet with id=AB6, first strand: chain 'I' and resid 207 through 209 Processing sheet with id=AB7, first strand: chain 'I' and resid 229 through 234 removed outlier: 7.769A pdb=" N CYS I 250 " --> pdb=" O THR I 263 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N THR I 263 " --> pdb=" O CYS I 250 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU I 252 " --> pdb=" O LEU I 261 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 273 through 277 removed outlier: 6.554A pdb=" N GLY I 288 " --> pdb=" O THR I 274 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL I 276 " --> pdb=" O LEU I 286 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU I 286 " --> pdb=" O VAL I 276 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA I 287 " --> pdb=" O ASN I 295 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN I 295 " --> pdb=" O ALA I 287 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ASP I 298 " --> pdb=" O ARG I 304 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ARG I 304 " --> pdb=" O ASP I 298 " (cutoff:3.500A) 1788 hydrogen bonds defined for protein. 5312 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: 6.83 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 16 1.05 - 1.26: 5627 1.26 - 1.47: 14380 1.47 - 1.69: 15812 1.69 - 1.90: 465 Bond restraints: 36300 Sorted by residual: bond pdb=" C03 9Z9 C1401 " pdb=" C74 9Z9 C1401 " ideal model delta sigma weight residual 1.534 0.831 0.703 2.00e-02 2.50e+03 1.24e+03 bond pdb=" C03 9Z9 A1403 " pdb=" C74 9Z9 A1403 " ideal model delta sigma weight residual 1.534 0.833 0.701 2.00e-02 2.50e+03 1.23e+03 bond pdb=" C03 9Z9 C1403 " pdb=" C74 9Z9 C1403 " ideal model delta sigma weight residual 1.534 0.835 0.699 2.00e-02 2.50e+03 1.22e+03 bond pdb=" C03 9Z9 B1401 " pdb=" C74 9Z9 B1401 " ideal model delta sigma weight residual 1.534 0.836 0.698 2.00e-02 2.50e+03 1.22e+03 bond pdb=" C02 9Z9 C1401 " pdb=" C03 9Z9 C1401 " ideal model delta sigma weight residual 1.544 1.012 0.532 2.00e-02 2.50e+03 7.07e+02 ... (remaining 36295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.33: 49069 10.33 - 20.66: 13 20.66 - 30.98: 8 30.98 - 41.31: 4 41.31 - 51.64: 4 Bond angle restraints: 49098 Sorted by residual: angle pdb=" C74 9Z9 B1401 " pdb=" C73 9Z9 B1401 " pdb=" C76 9Z9 B1401 " ideal model delta sigma weight residual 114.05 165.69 -51.64 3.00e+00 1.11e-01 2.96e+02 angle pdb=" C74 9Z9 C1403 " pdb=" C73 9Z9 C1403 " pdb=" C76 9Z9 C1403 " ideal model delta sigma weight residual 114.05 165.39 -51.34 3.00e+00 1.11e-01 2.93e+02 angle pdb=" C74 9Z9 C1401 " pdb=" C73 9Z9 C1401 " pdb=" C76 9Z9 C1401 " ideal model delta sigma weight residual 114.05 165.30 -51.25 3.00e+00 1.11e-01 2.92e+02 angle pdb=" C74 9Z9 A1403 " pdb=" C73 9Z9 A1403 " pdb=" C76 9Z9 A1403 " ideal model delta sigma weight residual 114.05 165.29 -51.24 3.00e+00 1.11e-01 2.92e+02 angle pdb=" C76 9Z9 C1401 " pdb=" C73 9Z9 C1401 " pdb=" O72 9Z9 C1401 " ideal model delta sigma weight residual 109.02 70.23 38.79 3.00e+00 1.11e-01 1.67e+02 ... (remaining 49093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.38: 20651 25.38 - 50.75: 881 50.75 - 76.13: 121 76.13 - 101.51: 6 101.51 - 126.89: 4 Dihedral angle restraints: 21663 sinusoidal: 8945 harmonic: 12718 Sorted by residual: dihedral pdb=" CA THR D 356 " pdb=" C THR D 356 " pdb=" N PRO D 357 " pdb=" CA PRO D 357 " ideal model delta harmonic sigma weight residual 180.00 154.49 25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA THR A 356 " pdb=" C THR A 356 " pdb=" N PRO A 357 " pdb=" CA PRO A 357 " ideal model delta harmonic sigma weight residual 180.00 155.65 24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA THR B 356 " pdb=" C THR B 356 " pdb=" N PRO B 357 " pdb=" CA PRO B 357 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 21660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.397: 5475 0.397 - 0.793: 4 0.793 - 1.190: 4 1.190 - 1.586: 0 1.586 - 1.983: 4 Chirality restraints: 5487 Sorted by residual: chirality pdb=" C03 9Z9 C1401 " pdb=" C02 9Z9 C1401 " pdb=" C04 9Z9 C1401 " pdb=" C74 9Z9 C1401 " both_signs ideal model delta sigma weight residual False 2.78 0.80 1.98 2.00e-01 2.50e+01 9.83e+01 chirality pdb=" C03 9Z9 A1403 " pdb=" C02 9Z9 A1403 " pdb=" C04 9Z9 A1403 " pdb=" C74 9Z9 A1403 " both_signs ideal model delta sigma weight residual False 2.78 0.83 1.95 2.00e-01 2.50e+01 9.51e+01 chirality pdb=" C03 9Z9 C1403 " pdb=" C02 9Z9 C1403 " pdb=" C04 9Z9 C1403 " pdb=" C74 9Z9 C1403 " both_signs ideal model delta sigma weight residual False 2.78 0.84 1.94 2.00e-01 2.50e+01 9.45e+01 ... (remaining 5484 not shown) Planarity restraints: 6105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 784 " 0.059 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO C 785 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 785 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 785 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 784 " -0.039 5.00e-02 4.00e+02 5.85e-02 5.47e+00 pdb=" N PRO D 785 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 785 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 785 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 590 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO D 591 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO D 591 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 591 " -0.030 5.00e-02 4.00e+02 ... (remaining 6102 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4164 2.75 - 3.29: 35245 3.29 - 3.82: 57296 3.82 - 4.36: 62862 4.36 - 4.90: 111600 Nonbonded interactions: 271167 Sorted by model distance: nonbonded pdb=" OD1 ASP B 947 " pdb=" OH TYR B 981 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR I 128 " pdb=" O ASN I 132 " model vdw 2.213 3.040 nonbonded pdb=" OG SER I 279 " pdb=" OD2 ASP J 48 " model vdw 2.222 3.040 nonbonded pdb=" N ASP B 559 " pdb=" OD1 ASP B 559 " model vdw 2.251 3.120 nonbonded pdb=" OG SER C 474 " pdb=" OE1 GLN C 475 " model vdw 2.254 3.040 ... (remaining 271162 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 129 through 1243) selection = (chain 'B' and resid 129 through 1243) selection = (chain 'C' and resid 129 through 1243) selection = (chain 'D' and (resid 129 through 588 or resid 632 through 1243)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.15 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 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: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.330 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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 : 0.014 0.703 36300 Z= 0.718 Angle : 0.999 51.641 49098 Z= 0.402 Chirality : 0.073 1.983 5487 Planarity : 0.004 0.088 6105 Dihedral : 13.494 126.885 13439 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.80 % Allowed : 8.95 % Favored : 87.25 % 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: -0.14 (0.13), residues: 4245 helix: 0.99 (0.11), residues: 2457 sheet: -0.41 (0.31), residues: 312 loop : -1.89 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 972 TYR 0.014 0.001 TYR C 380 PHE 0.012 0.001 PHE A1140 TRP 0.014 0.001 TRP C 763 HIS 0.003 0.001 HIS C 293 Details of bonding type rmsd/Z covalent geometry : bond 0.01441 / 0.72 (36300) covalent geometry : angle 0.99906 / 0.40 (49098) hydrogen bonds : bond 0.17007 / 11.32 ( 1788) hydrogen bonds : angle 5.26737 / 3.81 ( 5312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 510 time to evaluate : 1.081 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 918 GLU cc_start: 0.8488 (tp30) cc_final: 0.8131 (tp30) REVERT: A 955 SER cc_start: 0.8725 (m) cc_final: 0.8517 (p) REVERT: B 291 HIS cc_start: 0.8422 (OUTLIER) cc_final: 0.7892 (m170) REVERT: B 411 GLN cc_start: 0.7710 (tp-100) cc_final: 0.7205 (tt0) REVERT: B 432 MET cc_start: 0.7721 (mtm) cc_final: 0.7435 (mtm) REVERT: B 577 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8832 (m) REVERT: B 964 ASP cc_start: 0.4873 (p0) cc_final: 0.4577 (p0) REVERT: B 1002 MET cc_start: 0.7982 (mtt) cc_final: 0.7723 (mtt) REVERT: B 1017 MET cc_start: 0.8071 (tmm) cc_final: 0.7444 (mtp) REVERT: B 1186 THR cc_start: 0.7214 (OUTLIER) cc_final: 0.6716 (p) REVERT: C 192 LEU cc_start: 0.7144 (mp) cc_final: 0.6795 (tt) REVERT: C 198 GLN cc_start: 0.7571 (pm20) cc_final: 0.7338 (mp10) REVERT: C 214 MET cc_start: 0.7532 (tmm) cc_final: 0.7209 (tmm) REVERT: C 281 MET cc_start: 0.7994 (mmt) cc_final: 0.7785 (mmp) REVERT: C 290 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7928 (mmm) REVERT: C 380 TYR cc_start: 0.7703 (p90) cc_final: 0.7327 (p90) REVERT: C 405 TYR cc_start: 0.4824 (OUTLIER) cc_final: 0.3761 (p90) REVERT: C 492 MET cc_start: 0.9152 (mmm) cc_final: 0.8244 (tpp) REVERT: C 730 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.7962 (mtmm) REVERT: C 932 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6457 (tm) REVERT: D 258 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8249 (mm) REVERT: D 421 MET cc_start: 0.7926 (tpp) cc_final: 0.7554 (mmt) REVERT: D 453 ASN cc_start: 0.7302 (m-40) cc_final: 0.7064 (m110) REVERT: D 471 ILE cc_start: 0.8908 (mm) cc_final: 0.8692 (tt) REVERT: D 475 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.6887 (mp10) REVERT: D 510 ASN cc_start: 0.8207 (t0) cc_final: 0.7720 (t0) REVERT: D 593 ARG cc_start: 0.7225 (tpp-160) cc_final: 0.6743 (mmp-170) REVERT: D 642 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8099 (ttm) REVERT: D 687 MET cc_start: 0.7442 (tpp) cc_final: 0.7086 (tpp) REVERT: D 724 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9311 (tt) REVERT: D 1032 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7829 (mp) REVERT: D 1230 MET cc_start: 0.9033 (ttp) cc_final: 0.8586 (ttp) REVERT: I 99 TRP cc_start: 0.5702 (m-90) cc_final: 0.5359 (m100) REVERT: I 124 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.6417 (m-10) REVERT: J 27 ARG cc_start: 0.2711 (mtt90) cc_final: 0.1685 (ptp90) outliers start: 144 outliers final: 53 residues processed: 627 average time/residue: 0.2012 time to fit residues: 207.8938 Evaluate side-chains 435 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 369 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1186 THR Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 405 TYR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 554 ARG Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 1006 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 522 ARG Chi-restraints excluded: chain D residue 559 ASP Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 1032 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 124 TYR Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 225 HIS Chi-restraints excluded: chain I residue 263 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.0470 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 0.0470 chunk 424 optimal weight: 0.3980 chunk 155 optimal weight: 7.9990 overall best weight: 1.0578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 HIS A 314 GLN A 481 GLN A 719 GLN A 993 ASN ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN A1161 GLN A1238 ASN A1242 HIS B 151 HIS ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS B 314 GLN B 330 GLN B 490 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 HIS B 963 GLN B 978 ASN B1238 ASN C 178 GLN C 378 HIS C 411 GLN C 437 HIS C 633 HIS C 697 HIS C 719 GLN C 734 ASN C 963 GLN C 965 GLN ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 ASN C1242 HIS D 171 HIS D 232 HIS D 314 GLN D 378 HIS D 411 GLN D 734 ASN D 746 HIS D 890 ASN D 965 GLN D 978 ASN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1161 GLN D1194 HIS I 44 GLN I 110 ASN I 119 ASN I 230 ASN ** I 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.114680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.088206 restraints weight = 94071.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.090690 restraints weight = 58207.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.091590 restraints weight = 41372.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.092531 restraints weight = 33656.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.092686 restraints weight = 29653.406| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (21 function evaluations) r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36300 Z= 0.141 Angle : 0.590 10.678 49098 Z= 0.297 Chirality : 0.040 0.169 5487 Planarity : 0.004 0.048 6105 Dihedral : 9.325 121.489 5083 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.35 % Allowed : 12.25 % Favored : 84.40 % 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: 0.31 (0.13), residues: 4245 helix: 1.45 (0.11), residues: 2466 sheet: -0.56 (0.29), residues: 323 loop : -1.83 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 231 TYR 0.025 0.001 TYR D 553 PHE 0.020 0.001 PHE A 877 TRP 0.014 0.001 TRP A 763 HIS 0.018 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (36300) covalent geometry : angle 0.58951 / 0.30 (49098) hydrogen bonds : bond 0.05092 / 3.41 ( 1788) hydrogen bonds : angle 4.10452 / 2.96 ( 5312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 409 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 MET cc_start: 0.7164 (mmm) cc_final: 0.6863 (mmm) REVERT: A 432 MET cc_start: 0.6881 (pmm) cc_final: 0.6299 (mmm) REVERT: A 775 LEU cc_start: 0.8552 (pt) cc_final: 0.8034 (tt) REVERT: A 882 TYR cc_start: 0.8855 (t80) cc_final: 0.8514 (t80) REVERT: A 918 GLU cc_start: 0.8507 (tp30) cc_final: 0.8076 (tp30) REVERT: A 955 SER cc_start: 0.8788 (m) cc_final: 0.8531 (p) REVERT: A 965 GLN cc_start: 0.6508 (tm-30) cc_final: 0.5934 (pt0) REVERT: A 1095 MET cc_start: 0.6346 (mtp) cc_final: 0.6063 (mtp) REVERT: B 291 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.7981 (m170) REVERT: B 411 GLN cc_start: 0.7685 (tp-100) cc_final: 0.7246 (tt0) REVERT: B 577 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8714 (m) REVERT: B 729 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8799 (mm) REVERT: B 983 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7456 (t80) REVERT: B 1017 MET cc_start: 0.8088 (tmm) cc_final: 0.7690 (mtm) REVERT: B 1195 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7881 (t0) REVERT: B 1230 MET cc_start: 0.8422 (ttm) cc_final: 0.8013 (mtp) REVERT: C 192 LEU cc_start: 0.7258 (mp) cc_final: 0.6909 (tt) REVERT: C 198 GLN cc_start: 0.7594 (pm20) cc_final: 0.7363 (mp10) REVERT: C 214 MET cc_start: 0.7716 (tmm) cc_final: 0.7269 (tmm) REVERT: C 281 MET cc_start: 0.7965 (mmt) cc_final: 0.7726 (ptp) REVERT: C 290 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7791 (mmm) REVERT: C 405 TYR cc_start: 0.4776 (OUTLIER) cc_final: 0.3659 (p90) REVERT: C 418 MET cc_start: 0.7481 (ppp) cc_final: 0.6407 (ptt) REVERT: C 730 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8109 (mtmm) REVERT: C 920 MET cc_start: 0.7721 (mtm) cc_final: 0.7331 (ttm) REVERT: C 983 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.7243 (t80) REVERT: D 277 MET cc_start: 0.7502 (ppp) cc_final: 0.7206 (ppp) REVERT: D 374 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7996 (tm) REVERT: D 417 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8624 (tt) REVERT: D 421 MET cc_start: 0.7996 (tpp) cc_final: 0.7726 (mmt) REVERT: D 430 PHE cc_start: 0.8709 (t80) cc_final: 0.8492 (t80) REVERT: D 453 ASN cc_start: 0.7343 (m-40) cc_final: 0.7088 (m110) REVERT: D 475 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7146 (mp10) REVERT: D 593 ARG cc_start: 0.7311 (tpp-160) cc_final: 0.6748 (mmp-170) REVERT: D 642 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.7999 (tmm) REVERT: D 687 MET cc_start: 0.7350 (tpp) cc_final: 0.7058 (tpp) REVERT: D 701 ASP cc_start: 0.7804 (m-30) cc_final: 0.7365 (m-30) REVERT: D 1010 MET cc_start: 0.7347 (ttp) cc_final: 0.6993 (ptt) REVERT: D 1032 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7721 (mp) REVERT: I 124 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.7033 (m-10) REVERT: I 289 TYR cc_start: 0.5371 (m-80) cc_final: 0.4968 (m-80) REVERT: I 325 MET cc_start: 0.3062 (pmm) cc_final: 0.2620 (pmm) REVERT: J 27 ARG cc_start: 0.1632 (mtt90) cc_final: 0.0679 (ptp90) outliers start: 127 outliers final: 68 residues processed: 515 average time/residue: 0.1870 time to fit residues: 162.0390 Evaluate side-chains 447 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 364 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 963 GLN Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 405 TYR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 554 ARG Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 963 GLN Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 522 ARG Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1032 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 124 TYR Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 225 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 115 optimal weight: 4.9990 chunk 428 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 379 optimal weight: 3.9990 chunk 360 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 248 optimal weight: 0.0050 chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN B 890 ASN C 437 HIS ** C 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1199 GLN D 575 ASN D 731 ASN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.113624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.087675 restraints weight = 93476.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089390 restraints weight = 60336.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.090201 restraints weight = 49140.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.091111 restraints weight = 39008.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.091410 restraints weight = 33658.989| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (17 function evaluations) r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36300 Z= 0.176 Angle : 0.594 10.057 49098 Z= 0.297 Chirality : 0.040 0.165 5487 Planarity : 0.004 0.047 6105 Dihedral : 9.030 118.536 5055 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.01 % Allowed : 13.20 % Favored : 82.79 % 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: 0.34 (0.13), residues: 4245 helix: 1.48 (0.11), residues: 2479 sheet: -0.53 (0.28), residues: 324 loop : -1.87 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 256 TYR 0.017 0.001 TYR C 981 PHE 0.030 0.001 PHE A 877 TRP 0.025 0.001 TRP I 99 HIS 0.016 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (36300) covalent geometry : angle 0.59430 / 0.30 (49098) hydrogen bonds : bond 0.05115 / 3.44 ( 1788) hydrogen bonds : angle 4.03170 / 2.90 ( 5312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 371 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 MET cc_start: 0.7167 (mmm) cc_final: 0.6949 (mmm) REVERT: A 432 MET cc_start: 0.6952 (pmm) cc_final: 0.6410 (mmm) REVERT: A 510 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8829 (m-40) REVERT: A 559 ASP cc_start: 0.6590 (m-30) cc_final: 0.6367 (m-30) REVERT: A 687 MET cc_start: 0.5357 (mmp) cc_final: 0.5027 (mmm) REVERT: A 694 GLU cc_start: 0.8115 (tp30) cc_final: 0.7779 (tp30) REVERT: A 775 LEU cc_start: 0.8567 (pt) cc_final: 0.8054 (tt) REVERT: A 955 SER cc_start: 0.8802 (m) cc_final: 0.8562 (p) REVERT: A 1095 MET cc_start: 0.6284 (mtp) cc_final: 0.6007 (mtp) REVERT: A 1241 GLU cc_start: 0.1238 (OUTLIER) cc_final: -0.0549 (pm20) REVERT: B 577 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8784 (m) REVERT: B 729 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8816 (mm) REVERT: B 983 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7494 (t80) REVERT: B 1017 MET cc_start: 0.8154 (tmm) cc_final: 0.7624 (mtt) REVERT: B 1140 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8834 (t80) REVERT: B 1150 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7794 (pt) REVERT: B 1156 MET cc_start: 0.8446 (mtp) cc_final: 0.7956 (mtp) REVERT: B 1195 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7904 (t0) REVERT: C 192 LEU cc_start: 0.7232 (mp) cc_final: 0.6803 (tt) REVERT: C 198 GLN cc_start: 0.7655 (pm20) cc_final: 0.7399 (mp10) REVERT: C 214 MET cc_start: 0.7733 (tmm) cc_final: 0.7258 (tmm) REVERT: C 290 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7865 (mmm) REVERT: C 405 TYR cc_start: 0.4836 (OUTLIER) cc_final: 0.3723 (p90) REVERT: C 418 MET cc_start: 0.7485 (ppp) cc_final: 0.6442 (ptt) REVERT: C 568 MET cc_start: 0.8264 (mmm) cc_final: 0.7939 (mmm) REVERT: C 730 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8182 (mtmm) REVERT: C 983 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.7330 (t80) REVERT: C 1053 MET cc_start: 0.8889 (ttm) cc_final: 0.8593 (ttm) REVERT: C 1095 MET cc_start: 0.7681 (ttp) cc_final: 0.7439 (ttp) REVERT: C 1230 MET cc_start: 0.8193 (ttm) cc_final: 0.7988 (ttm) REVERT: D 172 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8701 (pp) REVERT: D 258 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8201 (mm) REVERT: D 374 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8074 (tm) REVERT: D 417 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8510 (tt) REVERT: D 453 ASN cc_start: 0.7332 (m-40) cc_final: 0.7069 (m110) REVERT: D 475 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7259 (mp10) REVERT: D 593 ARG cc_start: 0.7237 (tpp-160) cc_final: 0.6677 (mmp-170) REVERT: D 642 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7967 (tmm) REVERT: D 687 MET cc_start: 0.7367 (tpp) cc_final: 0.7015 (tpp) REVERT: D 701 ASP cc_start: 0.7818 (m-30) cc_final: 0.7354 (m-30) REVERT: D 1032 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7816 (mp) REVERT: I 95 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6922 (mm) REVERT: I 124 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.7063 (m-10) REVERT: I 289 TYR cc_start: 0.5526 (m-80) cc_final: 0.4985 (m-80) REVERT: J 27 ARG cc_start: 0.1390 (mtt90) cc_final: 0.0509 (ptp90) outliers start: 152 outliers final: 89 residues processed: 500 average time/residue: 0.1959 time to fit residues: 166.2019 Evaluate side-chains 463 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 353 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1241 GLU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1140 PHE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1232 MET Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 249 CYS Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 405 TYR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 554 ARG Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 522 ARG Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 920 MET Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 1032 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1227 VAL Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 124 TYR Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 225 HIS Chi-restraints excluded: chain I residue 335 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 387 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 381 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 382 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 369 optimal weight: 0.8980 chunk 411 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 HIS ** C 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1213 ASN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 266 HIS I 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.114318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087460 restraints weight = 108936.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.090737 restraints weight = 61944.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091552 restraints weight = 38989.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.091821 restraints weight = 33155.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.091868 restraints weight = 31130.790| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (25 function evaluations) r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36300 Z= 0.123 Angle : 0.553 11.137 49098 Z= 0.275 Chirality : 0.038 0.155 5487 Planarity : 0.004 0.050 6105 Dihedral : 8.798 114.367 5048 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.46 % Allowed : 14.49 % Favored : 82.05 % 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: 0.52 (0.13), residues: 4245 helix: 1.65 (0.11), residues: 2478 sheet: -0.54 (0.28), residues: 324 loop : -1.82 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1206 TYR 0.016 0.001 TYR C 981 PHE 0.040 0.001 PHE A 877 TRP 0.026 0.001 TRP I 99 HIS 0.013 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (36300) covalent geometry : angle 0.55339 / 0.27 (49098) hydrogen bonds : bond 0.04529 / 3.05 ( 1788) hydrogen bonds : angle 3.83773 / 2.76 ( 5312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 384 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 MET cc_start: 0.7201 (mmm) cc_final: 0.6864 (mmm) REVERT: A 432 MET cc_start: 0.6940 (pmm) cc_final: 0.6474 (mmm) REVERT: A 559 ASP cc_start: 0.6553 (m-30) cc_final: 0.6350 (m-30) REVERT: A 687 MET cc_start: 0.5599 (mmp) cc_final: 0.5321 (mmm) REVERT: A 775 LEU cc_start: 0.8588 (pt) cc_final: 0.8100 (tt) REVERT: A 955 SER cc_start: 0.8778 (m) cc_final: 0.8501 (p) REVERT: A 965 GLN cc_start: 0.6840 (tm-30) cc_final: 0.6304 (pt0) REVERT: A 1241 GLU cc_start: 0.0886 (OUTLIER) cc_final: -0.0850 (pm20) REVERT: B 577 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8757 (m) REVERT: B 729 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8795 (mm) REVERT: B 983 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7522 (t80) REVERT: B 1017 MET cc_start: 0.8051 (tmm) cc_final: 0.7688 (mtm) REVERT: B 1150 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7710 (pt) REVERT: B 1195 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7906 (t0) REVERT: C 192 LEU cc_start: 0.7143 (mp) cc_final: 0.6820 (tt) REVERT: C 198 GLN cc_start: 0.7679 (pm20) cc_final: 0.7445 (mp10) REVERT: C 214 MET cc_start: 0.7825 (tmm) cc_final: 0.7310 (tmm) REVERT: C 290 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7764 (mmm) REVERT: C 405 TYR cc_start: 0.4873 (OUTLIER) cc_final: 0.3916 (p90) REVERT: C 418 MET cc_start: 0.7436 (ppp) cc_final: 0.6420 (ptt) REVERT: C 568 MET cc_start: 0.8319 (mmm) cc_final: 0.8089 (mmm) REVERT: C 642 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7927 (tmm) REVERT: C 730 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8148 (mtmm) REVERT: C 983 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7220 (t80) REVERT: C 1230 MET cc_start: 0.8409 (ttm) cc_final: 0.8205 (ttm) REVERT: D 172 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8699 (pp) REVERT: D 258 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8190 (mm) REVERT: D 374 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7950 (tm) REVERT: D 407 ARG cc_start: 0.7125 (mmp-170) cc_final: 0.6788 (mmp80) REVERT: D 417 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8465 (tt) REVERT: D 453 ASN cc_start: 0.7303 (m-40) cc_final: 0.7015 (m110) REVERT: D 475 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7304 (mp10) REVERT: D 593 ARG cc_start: 0.7221 (tpp-160) cc_final: 0.6639 (mmp-170) REVERT: D 642 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8022 (tmm) REVERT: D 687 MET cc_start: 0.7249 (tpp) cc_final: 0.6867 (tpp) REVERT: D 701 ASP cc_start: 0.7783 (m-30) cc_final: 0.7276 (m-30) REVERT: D 1010 MET cc_start: 0.7525 (ttp) cc_final: 0.7236 (ptt) REVERT: D 1032 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7737 (mp) REVERT: D 1230 MET cc_start: 0.9141 (ttp) cc_final: 0.8700 (ttp) REVERT: I 95 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6880 (mm) REVERT: I 289 TYR cc_start: 0.5513 (m-80) cc_final: 0.4995 (m-80) REVERT: J 27 ARG cc_start: 0.1590 (mtt90) cc_final: 0.0721 (ptp90) outliers start: 131 outliers final: 83 residues processed: 492 average time/residue: 0.2124 time to fit residues: 175.7635 Evaluate side-chains 460 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 358 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1241 GLU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 900 TRP Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 405 TYR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 554 ARG Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 437 HIS Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 522 ARG Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain D residue 920 MET Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1032 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 225 HIS Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 335 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 144 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 396 optimal weight: 10.0000 chunk 159 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 253 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 398 optimal weight: 6.9990 chunk 134 optimal weight: 0.5980 chunk 150 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS D 575 ASN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.112959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.086872 restraints weight = 93888.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.088984 restraints weight = 58181.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.089642 restraints weight = 44742.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.090911 restraints weight = 36776.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.090882 restraints weight = 31091.536| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 36300 Z= 0.167 Angle : 0.583 10.093 49098 Z= 0.291 Chirality : 0.040 0.202 5487 Planarity : 0.004 0.049 6105 Dihedral : 8.689 112.123 5043 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.06 % Allowed : 14.89 % Favored : 81.05 % 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: 0.48 (0.13), residues: 4245 helix: 1.62 (0.11), residues: 2482 sheet: -0.58 (0.28), residues: 324 loop : -1.85 (0.16), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 580 TYR 0.018 0.001 TYR C 981 PHE 0.048 0.001 PHE A 877 TRP 0.027 0.001 TRP I 99 HIS 0.007 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (36300) covalent geometry : angle 0.58330 / 0.29 (49098) hydrogen bonds : bond 0.04882 / 3.28 ( 1788) hydrogen bonds : angle 3.90765 / 2.81 ( 5312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 360 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 MET cc_start: 0.7138 (mmm) cc_final: 0.6790 (mmm) REVERT: A 559 ASP cc_start: 0.6611 (m-30) cc_final: 0.6382 (m-30) REVERT: A 687 MET cc_start: 0.5763 (mmp) cc_final: 0.5417 (mmm) REVERT: A 694 GLU cc_start: 0.8133 (tp30) cc_final: 0.7907 (tp30) REVERT: A 775 LEU cc_start: 0.8603 (pt) cc_final: 0.8105 (tt) REVERT: A 882 TYR cc_start: 0.8978 (t80) cc_final: 0.8581 (t80) REVERT: A 955 SER cc_start: 0.8816 (m) cc_final: 0.8565 (p) REVERT: A 1241 GLU cc_start: 0.1250 (OUTLIER) cc_final: -0.0445 (pm20) REVERT: B 531 HIS cc_start: 0.7931 (OUTLIER) cc_final: 0.7435 (m90) REVERT: B 687 MET cc_start: 0.7145 (mmt) cc_final: 0.6940 (mmm) REVERT: B 729 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8781 (mm) REVERT: B 983 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7645 (t80) REVERT: B 1017 MET cc_start: 0.8124 (tmm) cc_final: 0.7615 (mtm) REVERT: B 1195 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7902 (t0) REVERT: C 192 LEU cc_start: 0.7193 (mp) cc_final: 0.6860 (tt) REVERT: C 214 MET cc_start: 0.7822 (tmm) cc_final: 0.7321 (tmm) REVERT: C 290 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7835 (mmm) REVERT: C 405 TYR cc_start: 0.4577 (OUTLIER) cc_final: 0.3876 (p90) REVERT: C 568 MET cc_start: 0.8294 (mmm) cc_final: 0.8042 (mmm) REVERT: C 642 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7932 (tmm) REVERT: C 730 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8171 (mtmm) REVERT: C 920 MET cc_start: 0.7632 (mtt) cc_final: 0.7425 (mtt) REVERT: C 925 MET cc_start: 0.6951 (tpt) cc_final: 0.6481 (tmm) REVERT: C 983 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7389 (t80) REVERT: D 172 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8702 (pp) REVERT: D 258 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8267 (mm) REVERT: D 374 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7731 (tm) REVERT: D 417 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8456 (tt) REVERT: D 430 PHE cc_start: 0.8529 (t80) cc_final: 0.8253 (t80) REVERT: D 453 ASN cc_start: 0.7232 (m-40) cc_final: 0.6928 (m110) REVERT: D 475 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7273 (mp10) REVERT: D 593 ARG cc_start: 0.7270 (tpp-160) cc_final: 0.6698 (mmp-170) REVERT: D 642 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8019 (tmm) REVERT: D 701 ASP cc_start: 0.7803 (m-30) cc_final: 0.7286 (m-30) REVERT: D 1010 MET cc_start: 0.7564 (ttp) cc_final: 0.7239 (ptt) REVERT: D 1032 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7890 (mp) REVERT: D 1158 MET cc_start: 0.7298 (tmm) cc_final: 0.7076 (tmm) REVERT: I 95 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6891 (mm) REVERT: I 289 TYR cc_start: 0.5718 (m-80) cc_final: 0.5287 (m-80) REVERT: J 27 ARG cc_start: 0.1561 (mtt90) cc_final: 0.0642 (ptp90) outliers start: 154 outliers final: 99 residues processed: 488 average time/residue: 0.2008 time to fit residues: 167.2040 Evaluate side-chains 459 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 342 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1241 GLU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 249 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 405 TYR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 437 HIS Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 522 ARG Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain D residue 920 MET Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 1032 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1227 VAL Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 225 HIS Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 335 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 61 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 305 optimal weight: 0.5980 chunk 223 optimal weight: 0.5980 chunk 261 optimal weight: 0.9990 chunk 374 optimal weight: 0.3980 chunk 368 optimal weight: 2.9990 chunk 416 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 313 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 ASN ** C 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 HIS ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 HIS ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.114987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.088184 restraints weight = 119511.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.090734 restraints weight = 66866.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.091872 restraints weight = 42762.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.092120 restraints weight = 37899.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092341 restraints weight = 34118.242| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 36300 Z= 0.110 Angle : 0.540 9.465 49098 Z= 0.268 Chirality : 0.038 0.158 5487 Planarity : 0.004 0.050 6105 Dihedral : 8.403 107.231 5036 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.17 % Allowed : 16.18 % Favored : 80.65 % 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: 0.69 (0.13), residues: 4245 helix: 1.80 (0.11), residues: 2484 sheet: -0.53 (0.28), residues: 324 loop : -1.78 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 407 TYR 0.020 0.001 TYR B 380 PHE 0.033 0.001 PHE A 877 TRP 0.022 0.001 TRP I 99 HIS 0.030 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (36300) covalent geometry : angle 0.54025 / 0.27 (49098) hydrogen bonds : bond 0.04158 / 2.80 ( 1788) hydrogen bonds : angle 3.67197 / 2.63 ( 5312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 372 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 MET cc_start: 0.7120 (mmm) cc_final: 0.6708 (mmm) REVERT: A 432 MET cc_start: 0.6898 (pmm) cc_final: 0.6386 (mmm) REVERT: A 559 ASP cc_start: 0.6444 (m-30) cc_final: 0.6237 (m-30) REVERT: A 687 MET cc_start: 0.5551 (mmp) cc_final: 0.5280 (mmm) REVERT: A 775 LEU cc_start: 0.8611 (pt) cc_final: 0.8120 (tt) REVERT: A 882 TYR cc_start: 0.8899 (t80) cc_final: 0.8593 (t80) REVERT: A 955 SER cc_start: 0.8781 (m) cc_final: 0.8491 (p) REVERT: A 965 GLN cc_start: 0.6877 (tm-30) cc_final: 0.6305 (pt0) REVERT: A 1108 ASN cc_start: 0.8240 (m-40) cc_final: 0.8029 (m-40) REVERT: A 1241 GLU cc_start: 0.0859 (OUTLIER) cc_final: -0.0714 (pm20) REVERT: B 729 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8788 (mm) REVERT: B 782 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6680 (mm) REVERT: B 983 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.7561 (t80) REVERT: B 1017 MET cc_start: 0.7978 (tmm) cc_final: 0.7705 (mtm) REVERT: B 1150 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7658 (pt) REVERT: B 1156 MET cc_start: 0.8028 (mtm) cc_final: 0.7820 (mtp) REVERT: B 1195 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7966 (t0) REVERT: C 192 LEU cc_start: 0.7128 (mp) cc_final: 0.6897 (tt) REVERT: C 214 MET cc_start: 0.7875 (tmm) cc_final: 0.7379 (tmm) REVERT: C 290 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7704 (mmm) REVERT: C 405 TYR cc_start: 0.4660 (OUTLIER) cc_final: 0.4036 (p90) REVERT: C 418 MET cc_start: 0.7331 (ppp) cc_final: 0.6434 (ptt) REVERT: C 568 MET cc_start: 0.8337 (mmm) cc_final: 0.8093 (mmm) REVERT: C 642 MET cc_start: 0.8390 (ttt) cc_final: 0.7942 (tmm) REVERT: C 730 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8128 (mtmm) REVERT: C 925 MET cc_start: 0.6935 (tpt) cc_final: 0.6485 (tmm) REVERT: C 983 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7271 (t80) REVERT: D 258 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8226 (mm) REVERT: D 407 ARG cc_start: 0.7137 (mmp-170) cc_final: 0.6827 (mmp80) REVERT: D 453 ASN cc_start: 0.7294 (m-40) cc_final: 0.6972 (m110) REVERT: D 475 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7284 (mp10) REVERT: D 642 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8054 (tmm) REVERT: D 701 ASP cc_start: 0.7814 (m-30) cc_final: 0.7269 (m-30) REVERT: D 769 MET cc_start: 0.6871 (OUTLIER) cc_final: 0.6644 (ppp) REVERT: D 1010 MET cc_start: 0.7532 (ttp) cc_final: 0.7278 (ptt) REVERT: D 1032 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7661 (mp) REVERT: I 95 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6897 (mm) REVERT: I 289 TYR cc_start: 0.5954 (m-80) cc_final: 0.5520 (m-80) REVERT: I 340 ASN cc_start: 0.4077 (t0) cc_final: 0.3655 (m-40) REVERT: J 27 ARG cc_start: 0.1913 (mtt90) cc_final: 0.1065 (ptp90) outliers start: 120 outliers final: 82 residues processed: 473 average time/residue: 0.2028 time to fit residues: 163.0154 Evaluate side-chains 452 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 354 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1241 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 900 TRP Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 249 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 405 TYR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 437 HIS Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 522 ARG Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain D residue 920 MET Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1032 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 225 HIS Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 335 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 292 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 chunk 278 optimal weight: 0.9990 chunk 153 optimal weight: 0.5980 chunk 399 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 GLN ** D1115 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 = 0.3660 r_free = 0.3660 target = 0.113646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.087297 restraints weight = 106037.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.089273 restraints weight = 62579.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.090911 restraints weight = 43204.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.091030 restraints weight = 38345.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.091158 restraints weight = 31755.567| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (19 function evaluations) r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36300 Z= 0.147 Angle : 0.572 14.159 49098 Z= 0.282 Chirality : 0.039 0.143 5487 Planarity : 0.004 0.050 6105 Dihedral : 8.315 105.417 5032 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.67 % Allowed : 15.97 % Favored : 80.36 % 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: 0.67 (0.13), residues: 4245 helix: 1.78 (0.11), residues: 2485 sheet: -0.52 (0.28), residues: 324 loop : -1.79 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 554 TYR 0.021 0.001 TYR B 380 PHE 0.030 0.001 PHE A 877 TRP 0.020 0.001 TRP I 99 HIS 0.010 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (36300) covalent geometry : angle 0.57155 / 0.28 (49098) hydrogen bonds : bond 0.04488 / 3.03 ( 1788) hydrogen bonds : angle 3.74595 / 2.68 ( 5312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 368 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 MET cc_start: 0.7107 (mmm) cc_final: 0.6816 (mmm) REVERT: A 432 MET cc_start: 0.6915 (pmm) cc_final: 0.6464 (mmm) REVERT: A 559 ASP cc_start: 0.6580 (m-30) cc_final: 0.6363 (m-30) REVERT: A 687 MET cc_start: 0.5547 (mmp) cc_final: 0.5326 (mmm) REVERT: A 694 GLU cc_start: 0.8063 (tp30) cc_final: 0.7782 (tp30) REVERT: A 775 LEU cc_start: 0.8608 (pt) cc_final: 0.8164 (tt) REVERT: A 882 TYR cc_start: 0.8961 (t80) cc_final: 0.8625 (t80) REVERT: A 955 SER cc_start: 0.8811 (m) cc_final: 0.8543 (p) REVERT: A 965 GLN cc_start: 0.6825 (tm-30) cc_final: 0.6204 (pt0) REVERT: A 1241 GLU cc_start: 0.0999 (OUTLIER) cc_final: -0.0587 (pm20) REVERT: B 296 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7796 (mp) REVERT: B 416 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.7144 (pt) REVERT: B 729 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8791 (mm) REVERT: B 963 GLN cc_start: 0.5889 (OUTLIER) cc_final: 0.5273 (tp40) REVERT: B 983 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.7627 (t80) REVERT: B 1017 MET cc_start: 0.8082 (tmm) cc_final: 0.7726 (mtm) REVERT: B 1150 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7765 (pt) REVERT: B 1195 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7911 (t0) REVERT: C 192 LEU cc_start: 0.7147 (mp) cc_final: 0.6877 (tt) REVERT: C 214 MET cc_start: 0.7782 (tmm) cc_final: 0.7371 (tmm) REVERT: C 290 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7731 (mmm) REVERT: C 405 TYR cc_start: 0.4693 (OUTLIER) cc_final: 0.3897 (p90) REVERT: C 418 MET cc_start: 0.7373 (ppp) cc_final: 0.6419 (ptt) REVERT: C 568 MET cc_start: 0.8349 (mmm) cc_final: 0.8094 (mmm) REVERT: C 642 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7977 (tmm) REVERT: C 730 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8227 (mtmm) REVERT: C 862 ARG cc_start: 0.5907 (tpt170) cc_final: 0.5080 (mmm-85) REVERT: C 925 MET cc_start: 0.6968 (tpt) cc_final: 0.6543 (tmm) REVERT: C 983 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7347 (t80) REVERT: D 172 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8703 (pp) REVERT: D 258 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8272 (mm) REVERT: D 421 MET cc_start: 0.7829 (mmt) cc_final: 0.7544 (mmt) REVERT: D 430 PHE cc_start: 0.8374 (t80) cc_final: 0.8167 (t80) REVERT: D 453 ASN cc_start: 0.7283 (m-40) cc_final: 0.6951 (m110) REVERT: D 475 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7310 (mp10) REVERT: D 642 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8006 (tmm) REVERT: D 701 ASP cc_start: 0.7836 (m-30) cc_final: 0.7282 (m-30) REVERT: D 1010 MET cc_start: 0.7532 (ttp) cc_final: 0.7268 (ptt) REVERT: D 1032 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7819 (mp) REVERT: D 1158 MET cc_start: 0.7281 (tmm) cc_final: 0.6993 (tmm) REVERT: I 95 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6916 (mm) REVERT: I 289 TYR cc_start: 0.5759 (m-80) cc_final: 0.5380 (m-80) REVERT: J 27 ARG cc_start: 0.1847 (mtt90) cc_final: 0.0951 (ptp90) outliers start: 139 outliers final: 97 residues processed: 480 average time/residue: 0.1989 time to fit residues: 163.0159 Evaluate side-chains 467 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 351 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1241 GLU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 963 GLN Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 249 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 405 TYR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 437 HIS Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 522 ARG Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain D residue 920 MET Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 1032 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1227 VAL Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 225 HIS Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 335 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 161 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 chunk 181 optimal weight: 0.5980 chunk 253 optimal weight: 0.9990 chunk 346 optimal weight: 4.9990 chunk 319 optimal weight: 4.9990 chunk 308 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 944 ASN ** C 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1115 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 = 0.3669 r_free = 0.3669 target = 0.114208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.088298 restraints weight = 108864.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.089427 restraints weight = 65688.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.090399 restraints weight = 47149.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.090792 restraints weight = 40988.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.090936 restraints weight = 37320.984| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36300 Z= 0.128 Angle : 0.568 9.398 49098 Z= 0.280 Chirality : 0.039 0.160 5487 Planarity : 0.004 0.051 6105 Dihedral : 8.180 102.523 5032 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.30 % Allowed : 16.86 % Favored : 79.84 % 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: 0.71 (0.13), residues: 4245 helix: 1.82 (0.11), residues: 2482 sheet: -0.53 (0.28), residues: 324 loop : -1.78 (0.16), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 407 TYR 0.016 0.001 TYR C 981 PHE 0.031 0.001 PHE A 877 TRP 0.022 0.001 TRP I 82 HIS 0.010 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (36300) covalent geometry : angle 0.56803 / 0.28 (49098) hydrogen bonds : bond 0.04336 / 2.92 ( 1788) hydrogen bonds : angle 3.70021 / 2.65 ( 5312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 366 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.7441 (mtt) cc_final: 0.7109 (mtp) REVERT: A 418 MET cc_start: 0.7200 (mmm) cc_final: 0.6847 (mmm) REVERT: A 432 MET cc_start: 0.6935 (pmm) cc_final: 0.6467 (mmm) REVERT: A 559 ASP cc_start: 0.6508 (m-30) cc_final: 0.6288 (m-30) REVERT: A 694 GLU cc_start: 0.8100 (tp30) cc_final: 0.7830 (tp30) REVERT: A 775 LEU cc_start: 0.8636 (pt) cc_final: 0.8190 (tt) REVERT: A 882 TYR cc_start: 0.8982 (t80) cc_final: 0.8680 (t80) REVERT: A 955 SER cc_start: 0.8805 (m) cc_final: 0.8523 (p) REVERT: A 1108 ASN cc_start: 0.8447 (m-40) cc_final: 0.8211 (m-40) REVERT: A 1241 GLU cc_start: 0.0809 (OUTLIER) cc_final: -0.0639 (pm20) REVERT: B 642 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8480 (tpp) REVERT: B 729 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8808 (mm) REVERT: B 963 GLN cc_start: 0.5920 (OUTLIER) cc_final: 0.5313 (tp40) REVERT: B 983 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.7607 (t80) REVERT: B 1017 MET cc_start: 0.8074 (tmm) cc_final: 0.7733 (mtm) REVERT: B 1150 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7673 (pt) REVERT: B 1195 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7955 (t0) REVERT: C 192 LEU cc_start: 0.7104 (mp) cc_final: 0.6858 (tt) REVERT: C 214 MET cc_start: 0.7754 (tmm) cc_final: 0.7352 (tmm) REVERT: C 290 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7695 (mmm) REVERT: C 405 TYR cc_start: 0.4629 (OUTLIER) cc_final: 0.3929 (p90) REVERT: C 418 MET cc_start: 0.7389 (ppp) cc_final: 0.6462 (ptt) REVERT: C 568 MET cc_start: 0.8306 (mmm) cc_final: 0.8050 (mmm) REVERT: C 642 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8030 (tmm) REVERT: C 730 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8181 (mtmm) REVERT: C 862 ARG cc_start: 0.5931 (tpt170) cc_final: 0.5070 (mmm-85) REVERT: C 925 MET cc_start: 0.6926 (tpt) cc_final: 0.6487 (tmm) REVERT: C 932 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6033 (tm) REVERT: C 983 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.7327 (t80) REVERT: D 172 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8714 (pp) REVERT: D 258 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8257 (mm) REVERT: D 412 HIS cc_start: 0.5583 (OUTLIER) cc_final: 0.5264 (p90) REVERT: D 421 MET cc_start: 0.7877 (mmt) cc_final: 0.7586 (mmt) REVERT: D 453 ASN cc_start: 0.7355 (m-40) cc_final: 0.7008 (m110) REVERT: D 475 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7328 (mp10) REVERT: D 642 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8047 (tmm) REVERT: D 701 ASP cc_start: 0.7794 (m-30) cc_final: 0.7259 (m-30) REVERT: D 1158 MET cc_start: 0.7282 (tmm) cc_final: 0.7023 (tmm) REVERT: I 95 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6927 (mm) REVERT: I 289 TYR cc_start: 0.6024 (m-80) cc_final: 0.5581 (m-80) REVERT: J 27 ARG cc_start: 0.1982 (mtt90) cc_final: 0.1092 (ptp90) outliers start: 125 outliers final: 96 residues processed: 467 average time/residue: 0.1932 time to fit residues: 153.0709 Evaluate side-chains 466 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 351 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1241 GLU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 944 ASN Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 963 GLN Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 249 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 405 TYR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 437 HIS Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 522 ARG Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1227 VAL Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 225 HIS Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 335 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 13 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 336 optimal weight: 0.0670 chunk 245 optimal weight: 1.9990 chunk 255 optimal weight: 3.9990 chunk 301 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 366 optimal weight: 0.6980 chunk 421 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 965 GLN ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 944 ASN ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.114441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.088757 restraints weight = 107918.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.089588 restraints weight = 64062.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.090731 restraints weight = 46670.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.091037 restraints weight = 41343.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.091140 restraints weight = 37475.892| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36300 Z= 0.122 Angle : 0.569 12.251 49098 Z= 0.279 Chirality : 0.039 0.157 5487 Planarity : 0.004 0.052 6105 Dihedral : 8.011 100.502 5026 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.35 % Allowed : 16.89 % Favored : 79.76 % 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: 0.75 (0.13), residues: 4245 helix: 1.86 (0.11), residues: 2482 sheet: -0.53 (0.28), residues: 324 loop : -1.77 (0.16), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 580 TYR 0.025 0.001 TYR B 380 PHE 0.026 0.001 PHE I 234 TRP 0.022 0.001 TRP I 82 HIS 0.011 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (36300) covalent geometry : angle 0.56927 / 0.28 (49098) hydrogen bonds : bond 0.04256 / 2.87 ( 1788) hydrogen bonds : angle 3.66126 / 2.62 ( 5312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 361 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.7462 (mtt) cc_final: 0.7178 (mtp) REVERT: A 418 MET cc_start: 0.7190 (mmm) cc_final: 0.6848 (mmm) REVERT: A 432 MET cc_start: 0.6919 (pmm) cc_final: 0.6474 (mmm) REVERT: A 559 ASP cc_start: 0.6451 (m-30) cc_final: 0.6233 (m-30) REVERT: A 694 GLU cc_start: 0.8038 (tp30) cc_final: 0.7772 (tp30) REVERT: A 775 LEU cc_start: 0.8595 (pt) cc_final: 0.8210 (tt) REVERT: A 882 TYR cc_start: 0.8986 (t80) cc_final: 0.8707 (t80) REVERT: A 955 SER cc_start: 0.8790 (m) cc_final: 0.8517 (p) REVERT: A 965 GLN cc_start: 0.6478 (OUTLIER) cc_final: 0.6082 (pt0) REVERT: A 1108 ASN cc_start: 0.8419 (m-40) cc_final: 0.8190 (m-40) REVERT: A 1241 GLU cc_start: 0.0789 (OUTLIER) cc_final: -0.0666 (pm20) REVERT: B 380 TYR cc_start: 0.4803 (t80) cc_final: 0.4447 (t80) REVERT: B 524 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6512 (mt-10) REVERT: B 642 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8436 (tpp) REVERT: B 729 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8795 (mm) REVERT: B 963 GLN cc_start: 0.5918 (OUTLIER) cc_final: 0.5287 (tp40) REVERT: B 983 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.7597 (t80) REVERT: B 1017 MET cc_start: 0.8036 (tmm) cc_final: 0.7748 (mtm) REVERT: B 1150 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7650 (pt) REVERT: B 1195 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7924 (t0) REVERT: C 192 LEU cc_start: 0.7111 (mp) cc_final: 0.6870 (tt) REVERT: C 214 MET cc_start: 0.7732 (tmm) cc_final: 0.7331 (tmm) REVERT: C 290 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7646 (mmm) REVERT: C 405 TYR cc_start: 0.4623 (OUTLIER) cc_final: 0.3921 (p90) REVERT: C 418 MET cc_start: 0.7404 (ppp) cc_final: 0.6477 (ptt) REVERT: C 568 MET cc_start: 0.8295 (mmm) cc_final: 0.8043 (mmm) REVERT: C 642 MET cc_start: 0.8464 (ttt) cc_final: 0.8021 (tmm) REVERT: C 730 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8192 (mtmm) REVERT: C 862 ARG cc_start: 0.5953 (tpt170) cc_final: 0.5106 (mmm-85) REVERT: C 925 MET cc_start: 0.6907 (tpt) cc_final: 0.6476 (tmm) REVERT: C 932 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6070 (tm) REVERT: C 983 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7301 (t80) REVERT: D 172 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8708 (pp) REVERT: D 258 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8246 (mm) REVERT: D 407 ARG cc_start: 0.7181 (mmp-170) cc_final: 0.6837 (mmp80) REVERT: D 412 HIS cc_start: 0.5597 (OUTLIER) cc_final: 0.5375 (p90) REVERT: D 421 MET cc_start: 0.7865 (mmt) cc_final: 0.7600 (mmt) REVERT: D 453 ASN cc_start: 0.7319 (m-40) cc_final: 0.6975 (m110) REVERT: D 475 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7327 (mp10) REVERT: D 642 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8017 (tmm) REVERT: D 701 ASP cc_start: 0.7813 (m-30) cc_final: 0.7266 (m-30) REVERT: D 1032 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7783 (mp) REVERT: D 1158 MET cc_start: 0.7215 (tmm) cc_final: 0.6971 (tmm) REVERT: I 95 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6930 (mm) REVERT: I 289 TYR cc_start: 0.6014 (m-80) cc_final: 0.5574 (m-80) REVERT: J 27 ARG cc_start: 0.1981 (mtt90) cc_final: 0.1102 (ptp90) outliers start: 127 outliers final: 101 residues processed: 462 average time/residue: 0.1906 time to fit residues: 149.5926 Evaluate side-chains 474 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 353 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1241 GLU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 944 ASN Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 963 GLN Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 249 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 405 TYR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 437 HIS Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 522 ARG Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain D residue 920 MET Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1032 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1227 VAL Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 225 HIS Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 335 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 373 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 0.0040 chunk 301 optimal weight: 4.9990 chunk 284 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 426 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 324 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 965 GLN ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.113811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.087480 restraints weight = 99183.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.090323 restraints weight = 58749.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.091045 restraints weight = 41952.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.091502 restraints weight = 33721.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.091732 restraints weight = 31845.748| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 36300 Z= 0.150 Angle : 0.592 10.905 49098 Z= 0.291 Chirality : 0.039 0.226 5487 Planarity : 0.004 0.052 6105 Dihedral : 7.980 99.532 5026 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.40 % Allowed : 17.13 % Favored : 79.47 % 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: 0.68 (0.13), residues: 4245 helix: 1.81 (0.11), residues: 2482 sheet: -0.51 (0.28), residues: 323 loop : -1.80 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 580 TYR 0.025 0.001 TYR B 380 PHE 0.037 0.001 PHE I 234 TRP 0.023 0.001 TRP I 82 HIS 0.011 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (36300) covalent geometry : angle 0.59245 / 0.29 (49098) hydrogen bonds : bond 0.04456 / 3.01 ( 1788) hydrogen bonds : angle 3.72342 / 2.66 ( 5312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8490 Ramachandran restraints generated. 4245 Oldfield, 0 Emsley, 4245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 357 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.7458 (mtt) cc_final: 0.7195 (mtp) REVERT: A 414 PHE cc_start: 0.6846 (t80) cc_final: 0.6581 (t80) REVERT: A 418 MET cc_start: 0.7133 (mmm) cc_final: 0.6663 (mmm) REVERT: A 432 MET cc_start: 0.6946 (pmm) cc_final: 0.6550 (mmm) REVERT: A 559 ASP cc_start: 0.6504 (m-30) cc_final: 0.6283 (m-30) REVERT: A 694 GLU cc_start: 0.8034 (tp30) cc_final: 0.7765 (tp30) REVERT: A 775 LEU cc_start: 0.8507 (pt) cc_final: 0.8129 (tt) REVERT: A 882 TYR cc_start: 0.9057 (t80) cc_final: 0.8736 (t80) REVERT: A 955 SER cc_start: 0.8805 (m) cc_final: 0.8529 (p) REVERT: A 1108 ASN cc_start: 0.8304 (m-40) cc_final: 0.8082 (m-40) REVERT: A 1241 GLU cc_start: 0.1018 (OUTLIER) cc_final: -0.0507 (pm20) REVERT: B 380 TYR cc_start: 0.4988 (t80) cc_final: 0.4623 (t80) REVERT: B 524 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6627 (mt-10) REVERT: B 642 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8438 (tpp) REVERT: B 729 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8768 (mm) REVERT: B 963 GLN cc_start: 0.5857 (OUTLIER) cc_final: 0.5268 (tp40) REVERT: B 983 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.7559 (t80) REVERT: B 1017 MET cc_start: 0.8131 (tmm) cc_final: 0.7715 (mtm) REVERT: B 1150 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7688 (pt) REVERT: B 1195 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7844 (t0) REVERT: C 192 LEU cc_start: 0.7144 (mp) cc_final: 0.6904 (tt) REVERT: C 214 MET cc_start: 0.7810 (tmm) cc_final: 0.7389 (tmm) REVERT: C 290 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7673 (mmm) REVERT: C 405 TYR cc_start: 0.4647 (OUTLIER) cc_final: 0.3903 (p90) REVERT: C 418 MET cc_start: 0.7309 (ppp) cc_final: 0.6404 (ptt) REVERT: C 568 MET cc_start: 0.8322 (mmm) cc_final: 0.8039 (mmm) REVERT: C 642 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8044 (tmm) REVERT: C 730 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8231 (mtmm) REVERT: C 862 ARG cc_start: 0.5966 (tpt170) cc_final: 0.5127 (mmm-85) REVERT: C 925 MET cc_start: 0.6878 (tpt) cc_final: 0.6495 (tmm) REVERT: C 932 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6055 (tm) REVERT: C 983 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.7347 (t80) REVERT: D 172 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8683 (pp) REVERT: D 258 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8283 (mm) REVERT: D 407 ARG cc_start: 0.7308 (mmp-170) cc_final: 0.6955 (mmp80) REVERT: D 421 MET cc_start: 0.7920 (mmt) cc_final: 0.7621 (mmt) REVERT: D 453 ASN cc_start: 0.7301 (m-40) cc_final: 0.6938 (m110) REVERT: D 475 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7361 (mp10) REVERT: D 600 LEU cc_start: 0.7848 (mm) cc_final: 0.7566 (mt) REVERT: D 642 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8042 (tmm) REVERT: D 701 ASP cc_start: 0.7768 (m-30) cc_final: 0.7244 (m-30) REVERT: D 775 LEU cc_start: 0.8572 (pt) cc_final: 0.8296 (mt) REVERT: D 1032 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7793 (mp) REVERT: D 1158 MET cc_start: 0.7179 (tmm) cc_final: 0.6916 (tmm) REVERT: I 95 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6895 (mm) REVERT: I 289 TYR cc_start: 0.6113 (m-80) cc_final: 0.5637 (m-80) REVERT: J 27 ARG cc_start: 0.1570 (mtt90) cc_final: 0.0676 (ptp90) outliers start: 129 outliers final: 102 residues processed: 457 average time/residue: 0.1949 time to fit residues: 151.3863 Evaluate side-chains 477 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 356 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1241 GLU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 944 ASN Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 963 GLN Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 249 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 405 TYR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 437 HIS Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 522 ARG Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain D residue 920 MET Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1032 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1227 VAL Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 225 HIS Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 335 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 311 optimal weight: 0.9990 chunk 341 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 332 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 chunk 88 optimal weight: 0.0980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 965 GLN ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 944 ASN ** C 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.114596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.088336 restraints weight = 92134.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.090949 restraints weight = 56025.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.091942 restraints weight = 38702.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.092678 restraints weight = 31462.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.092913 restraints weight = 28397.380| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (11 function evaluations) r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36300 Z= 0.119 Angle : 0.571 11.375 49098 Z= 0.280 Chirality : 0.039 0.197 5487 Planarity : 0.004 0.052 6105 Dihedral : 7.872 97.212 5026 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.40 % Allowed : 17.15 % Favored : 79.44 % 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: 0.75 (0.13), residues: 4245 helix: 1.87 (0.11), residues: 2481 sheet: -0.63 (0.28), residues: 329 loop : -1.77 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 580 TYR 0.024 0.001 TYR B 380 PHE 0.029 0.001 PHE I 234 TRP 0.024 0.001 TRP I 82 HIS 0.011 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (36300) covalent geometry : angle 0.57137 / 0.28 (49098) hydrogen bonds : bond 0.04210 / 2.84 ( 1788) hydrogen bonds : angle 3.63749 / 2.60 ( 5312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6250.36 seconds wall clock time: 108 minutes 48.75 seconds (6528.75 seconds total)