Starting phenix.real_space_refine on Mon Sep 14 12:19:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6bqr_7132/09_2026/6bqr_7132.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bqr_7132/09_2026/6bqr_7132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6bqr_7132/09_2026/6bqr_7132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bqr_7132/09_2026/6bqr_7132.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bqr_7132/09_2026/6bqr_7132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bqr_7132/09_2026/6bqr_7132.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6bqr_7132/09_2026/6bqr_7132.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6bqr_7132/09_2026/6bqr_7132.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 19492 2.51 5 N 5240 2.21 5 O 5228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30116 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7424 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 38, 'TRANS': 909} Chain breaks: 7 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 7424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7424 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 38, 'TRANS': 909} Chain breaks: 7 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 7424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7424 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 38, 'TRANS': 909} Chain breaks: 7 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 7424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7424 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 38, 'TRANS': 909} Chain breaks: 7 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.04, per 1000 atoms: 0.20 Number of scatterers: 30116 At special positions: 0 Unit cell: (144.348, 145.394, 158.992, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 5228 8.00 N 5240 7.00 C 19492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.05 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=2.05 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " distance=2.05 Simple disulfide: pdb=" SG CYS D 993 " - pdb=" SG CYS D1011 " distance=2.05 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: 2.57 Conformation dependent library (CDL) restraints added in 1.2 seconds 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6992 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 12 sheets defined 66.2% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.804A pdb=" N TYR A 103 " --> pdb=" O PRO A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.723A pdb=" N ALA A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 177 removed outlier: 4.109A pdb=" N HIS A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 260 removed outlier: 4.430A pdb=" N ARG A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.602A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 4.017A pdb=" N THR A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 4.628A pdb=" N ARG A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.687A pdb=" N LEU A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.504A pdb=" N LEU A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.747A pdb=" N ALA A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 removed outlier: 3.588A pdb=" N LEU A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 removed outlier: 3.764A pdb=" N VAL A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.612A pdb=" N ALA A 466 " --> pdb=" O GLN A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 483 removed outlier: 3.636A pdb=" N HIS A 482 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 559 through 569 Processing helix chain 'A' and resid 571 through 582 removed outlier: 3.534A pdb=" N MET A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 removed outlier: 3.694A pdb=" N ARG A 597 " --> pdb=" O CYS A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 632 removed outlier: 3.672A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.677A pdb=" N LEU A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.574A pdb=" N PHE A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 690 through 698 Processing helix chain 'A' and resid 699 through 704 Processing helix chain 'A' and resid 767 through 777 removed outlier: 3.733A pdb=" N ARG A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP A 772 " --> pdb=" O CYS A 768 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS A 774 " --> pdb=" O ARG A 770 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 775 " --> pdb=" O ARG A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 803 removed outlier: 3.739A pdb=" N TYR A 790 " --> pdb=" O ASN A 786 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 803 " --> pdb=" O ARG A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 835 removed outlier: 3.689A pdb=" N THR A 823 " --> pdb=" O PHE A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 860 removed outlier: 3.745A pdb=" N ARG A 857 " --> pdb=" O SER A 853 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 858 " --> pdb=" O GLN A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 884 removed outlier: 3.699A pdb=" N THR A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 910 removed outlier: 3.583A pdb=" N MET A 900 " --> pdb=" O CYS A 896 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 923 removed outlier: 3.513A pdb=" N ILE A 922 " --> pdb=" O PRO A 918 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 923 " --> pdb=" O LYS A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 952 Processing helix chain 'A' and resid 958 through 967 removed outlier: 3.618A pdb=" N ARG A 964 " --> pdb=" O PRO A 960 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 967 " --> pdb=" O LEU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 973 removed outlier: 3.643A pdb=" N GLN A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 976 No H-bonds generated for 'chain 'A' and resid 974 through 976' Processing helix chain 'A' and resid 979 through 984 Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 1016 through 1031 removed outlier: 3.532A pdb=" N VAL A1021 " --> pdb=" O ASN A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1072 removed outlier: 3.838A pdb=" N GLN A1051 " --> pdb=" O PHE A1047 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A1056 " --> pdb=" O GLY A1052 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA A1060 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS A1070 " --> pdb=" O ILE A1066 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1089 removed outlier: 3.503A pdb=" N ARG A1086 " --> pdb=" O ILE A1082 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A1087 " --> pdb=" O SER A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1142 removed outlier: 4.278A pdb=" N ARG A1119 " --> pdb=" O LYS A1115 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A1120 " --> pdb=" O GLU A1116 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG A1138 " --> pdb=" O LEU A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1164 removed outlier: 3.848A pdb=" N LEU A1157 " --> pdb=" O GLN A1153 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A1164 " --> pdb=" O LYS A1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.805A pdb=" N TYR B 103 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 141 through 150 removed outlier: 3.723A pdb=" N ALA B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 177 removed outlier: 4.109A pdb=" N HIS B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 260 removed outlier: 4.430A pdb=" N ARG B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.602A pdb=" N LEU B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN B 290 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 removed outlier: 4.017A pdb=" N THR B 314 " --> pdb=" O CYS B 310 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 4.628A pdb=" N ARG B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 358 removed outlier: 3.687A pdb=" N LEU B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 removed outlier: 3.504A pdb=" N LEU B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 403 Processing helix chain 'B' and resid 405 through 415 removed outlier: 3.747A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 removed outlier: 3.588A pdb=" N LEU B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 removed outlier: 3.764A pdb=" N VAL B 441 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.611A pdb=" N ALA B 466 " --> pdb=" O GLN B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 483 removed outlier: 3.637A pdb=" N HIS B 482 " --> pdb=" O ASP B 478 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 483 " --> pdb=" O GLN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 559 through 569 Processing helix chain 'B' and resid 571 through 582 removed outlier: 3.533A pdb=" N MET B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 603 removed outlier: 3.695A pdb=" N ARG B 597 " --> pdb=" O CYS B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 632 removed outlier: 3.673A pdb=" N ALA B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 619 " --> pdb=" O LEU B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 643 removed outlier: 3.677A pdb=" N LEU B 642 " --> pdb=" O ALA B 638 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 Processing helix chain 'B' and resid 663 through 669 removed outlier: 3.575A pdb=" N PHE B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 690 through 698 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 767 through 777 removed outlier: 3.733A pdb=" N ARG B 771 " --> pdb=" O ARG B 767 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP B 772 " --> pdb=" O CYS B 768 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS B 774 " --> pdb=" O ARG B 770 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE B 775 " --> pdb=" O ARG B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 803 removed outlier: 3.739A pdb=" N TYR B 790 " --> pdb=" O ASN B 786 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 803 " --> pdb=" O ARG B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 835 removed outlier: 3.689A pdb=" N THR B 823 " --> pdb=" O PHE B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 860 removed outlier: 3.745A pdb=" N ARG B 857 " --> pdb=" O SER B 853 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 858 " --> pdb=" O GLN B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 884 removed outlier: 3.699A pdb=" N THR B 884 " --> pdb=" O GLY B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 910 removed outlier: 3.583A pdb=" N MET B 900 " --> pdb=" O CYS B 896 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU B 907 " --> pdb=" O THR B 903 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 926 removed outlier: 3.514A pdb=" N ILE B 922 " --> pdb=" O PRO B 918 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 923 " --> pdb=" O LYS B 919 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS B 925 " --> pdb=" O VAL B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 952 Processing helix chain 'B' and resid 958 through 967 removed outlier: 3.617A pdb=" N ARG B 964 " --> pdb=" O PRO B 960 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 967 " --> pdb=" O LEU B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 973 removed outlier: 3.642A pdb=" N GLN B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 976 No H-bonds generated for 'chain 'B' and resid 974 through 976' Processing helix chain 'B' and resid 979 through 984 Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 1016 through 1031 removed outlier: 3.532A pdb=" N VAL B1021 " --> pdb=" O ASN B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1072 removed outlier: 3.838A pdb=" N GLN B1051 " --> pdb=" O PHE B1047 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY B1052 " --> pdb=" O GLY B1048 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN B1053 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B1056 " --> pdb=" O GLY B1052 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA B1060 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS B1070 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1089 removed outlier: 3.503A pdb=" N ARG B1086 " --> pdb=" O ILE B1082 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B1087 " --> pdb=" O SER B1083 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1142 removed outlier: 4.278A pdb=" N ARG B1119 " --> pdb=" O LYS B1115 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B1120 " --> pdb=" O GLU B1116 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG B1138 " --> pdb=" O LEU B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1164 removed outlier: 3.848A pdb=" N LEU B1157 " --> pdb=" O GLN B1153 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS B1164 " --> pdb=" O LYS B1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 108 removed outlier: 3.804A pdb=" N TYR C 103 " --> pdb=" O PRO C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 140 Processing helix chain 'C' and resid 141 through 150 removed outlier: 3.723A pdb=" N ALA C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C 149 " --> pdb=" O ALA C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 177 removed outlier: 4.109A pdb=" N HIS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 260 removed outlier: 4.430A pdb=" N ARG C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 removed outlier: 3.601A pdb=" N LEU C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN C 290 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 removed outlier: 4.017A pdb=" N THR C 314 " --> pdb=" O CYS C 310 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 4.628A pdb=" N ARG C 332 " --> pdb=" O GLN C 328 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP C 333 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE C 338 " --> pdb=" O ARG C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 358 removed outlier: 3.687A pdb=" N LEU C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL C 351 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 386 removed outlier: 3.504A pdb=" N LEU C 381 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 403 Processing helix chain 'C' and resid 405 through 415 removed outlier: 3.747A pdb=" N ALA C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 removed outlier: 3.588A pdb=" N LEU C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 427 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 431 " --> pdb=" O ALA C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 447 removed outlier: 3.763A pdb=" N VAL C 441 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 466 removed outlier: 3.613A pdb=" N ALA C 466 " --> pdb=" O GLN C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 483 removed outlier: 3.637A pdb=" N HIS C 482 " --> pdb=" O ASP C 478 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER C 483 " --> pdb=" O GLN C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 510 Processing helix chain 'C' and resid 559 through 569 Processing helix chain 'C' and resid 571 through 582 removed outlier: 3.534A pdb=" N MET C 576 " --> pdb=" O ALA C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 603 removed outlier: 3.695A pdb=" N ARG C 597 " --> pdb=" O CYS C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 632 removed outlier: 3.672A pdb=" N ALA C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE C 619 " --> pdb=" O LEU C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.677A pdb=" N LEU C 642 " --> pdb=" O ALA C 638 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 663 through 669 removed outlier: 3.574A pdb=" N PHE C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 690 through 698 Processing helix chain 'C' and resid 699 through 704 Processing helix chain 'C' and resid 767 through 777 removed outlier: 3.732A pdb=" N ARG C 771 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP C 772 " --> pdb=" O CYS C 768 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS C 774 " --> pdb=" O ARG C 770 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 775 " --> pdb=" O ARG C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 803 removed outlier: 3.739A pdb=" N TYR C 790 " --> pdb=" O ASN C 786 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 803 " --> pdb=" O ARG C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 835 removed outlier: 3.689A pdb=" N THR C 823 " --> pdb=" O PHE C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 860 removed outlier: 3.745A pdb=" N ARG C 857 " --> pdb=" O SER C 853 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 858 " --> pdb=" O GLN C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 884 removed outlier: 3.699A pdb=" N THR C 884 " --> pdb=" O GLY C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 910 removed outlier: 3.584A pdb=" N MET C 900 " --> pdb=" O CYS C 896 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 907 " --> pdb=" O THR C 903 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 923 removed outlier: 3.513A pdb=" N ILE C 922 " --> pdb=" O PRO C 918 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 923 " --> pdb=" O LYS C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 952 Processing helix chain 'C' and resid 958 through 967 removed outlier: 3.618A pdb=" N ARG C 964 " --> pdb=" O PRO C 960 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 967 " --> pdb=" O LEU C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 973 removed outlier: 3.642A pdb=" N GLN C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 976 No H-bonds generated for 'chain 'C' and resid 974 through 976' Processing helix chain 'C' and resid 979 through 984 Processing helix chain 'C' and resid 985 through 988 Processing helix chain 'C' and resid 1016 through 1031 removed outlier: 3.532A pdb=" N VAL C1021 " --> pdb=" O ASN C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1072 removed outlier: 3.839A pdb=" N GLN C1051 " --> pdb=" O PHE C1047 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY C1052 " --> pdb=" O GLY C1048 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN C1053 " --> pdb=" O LYS C1049 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C1056 " --> pdb=" O GLY C1052 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA C1060 " --> pdb=" O LEU C1056 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS C1070 " --> pdb=" O ILE C1066 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1089 removed outlier: 3.502A pdb=" N ARG C1086 " --> pdb=" O ILE C1082 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C1087 " --> pdb=" O SER C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1142 removed outlier: 4.279A pdb=" N ARG C1119 " --> pdb=" O LYS C1115 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C1120 " --> pdb=" O GLU C1116 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG C1138 " --> pdb=" O LEU C1134 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1164 removed outlier: 3.849A pdb=" N LEU C1157 " --> pdb=" O GLN C1153 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS C1164 " --> pdb=" O LYS C1160 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 108 removed outlier: 3.804A pdb=" N TYR D 103 " --> pdb=" O PRO D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 141 through 150 removed outlier: 3.723A pdb=" N ALA D 145 " --> pdb=" O GLY D 141 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR D 149 " --> pdb=" O ALA D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 177 removed outlier: 4.109A pdb=" N HIS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 260 removed outlier: 4.431A pdb=" N ARG D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 removed outlier: 3.602A pdb=" N LEU D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 removed outlier: 4.016A pdb=" N THR D 314 " --> pdb=" O CYS D 310 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 316 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 4.629A pdb=" N ARG D 332 " --> pdb=" O GLN D 328 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP D 333 " --> pdb=" O GLY D 329 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 335 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 358 removed outlier: 3.687A pdb=" N LEU D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D 353 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 removed outlier: 3.504A pdb=" N LEU D 381 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 405 through 415 removed outlier: 3.748A pdb=" N ALA D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 435 removed outlier: 3.588A pdb=" N LEU D 425 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 427 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 removed outlier: 3.765A pdb=" N VAL D 441 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 466 removed outlier: 3.612A pdb=" N ALA D 466 " --> pdb=" O GLN D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 removed outlier: 3.636A pdb=" N HIS D 482 " --> pdb=" O ASP D 478 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER D 483 " --> pdb=" O GLN D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 510 Processing helix chain 'D' and resid 559 through 569 Processing helix chain 'D' and resid 571 through 582 removed outlier: 3.534A pdb=" N MET D 576 " --> pdb=" O ALA D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 603 removed outlier: 3.694A pdb=" N ARG D 597 " --> pdb=" O CYS D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 632 removed outlier: 3.673A pdb=" N ALA D 609 " --> pdb=" O ASP D 605 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE D 619 " --> pdb=" O LEU D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 643 removed outlier: 3.678A pdb=" N LEU D 642 " --> pdb=" O ALA D 638 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 661 Processing helix chain 'D' and resid 663 through 669 removed outlier: 3.574A pdb=" N PHE D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 690 through 698 Processing helix chain 'D' and resid 699 through 704 Processing helix chain 'D' and resid 767 through 777 removed outlier: 3.733A pdb=" N ARG D 771 " --> pdb=" O ARG D 767 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP D 772 " --> pdb=" O CYS D 768 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS D 774 " --> pdb=" O ARG D 770 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 775 " --> pdb=" O ARG D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 803 removed outlier: 3.739A pdb=" N TYR D 790 " --> pdb=" O ASN D 786 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 835 removed outlier: 3.689A pdb=" N THR D 823 " --> pdb=" O PHE D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 860 removed outlier: 3.745A pdb=" N ARG D 857 " --> pdb=" O SER D 853 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU D 858 " --> pdb=" O GLN D 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 884 removed outlier: 3.699A pdb=" N THR D 884 " --> pdb=" O GLY D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 910 removed outlier: 3.583A pdb=" N MET D 900 " --> pdb=" O CYS D 896 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 907 " --> pdb=" O THR D 903 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS D 908 " --> pdb=" O VAL D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 926 removed outlier: 3.513A pdb=" N ILE D 922 " --> pdb=" O PRO D 918 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 923 " --> pdb=" O LYS D 919 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER D 924 " --> pdb=" O ILE D 920 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS D 925 " --> pdb=" O VAL D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 952 Processing helix chain 'D' and resid 958 through 967 removed outlier: 3.618A pdb=" N ARG D 964 " --> pdb=" O PRO D 960 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 967 " --> pdb=" O LEU D 963 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 973 removed outlier: 3.643A pdb=" N GLN D 973 " --> pdb=" O ARG D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 974 through 976 No H-bonds generated for 'chain 'D' and resid 974 through 976' Processing helix chain 'D' and resid 979 through 984 Processing helix chain 'D' and resid 985 through 988 Processing helix chain 'D' and resid 1016 through 1031 removed outlier: 3.531A pdb=" N VAL D1021 " --> pdb=" O ASN D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1072 removed outlier: 3.838A pdb=" N GLN D1051 " --> pdb=" O PHE D1047 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY D1052 " --> pdb=" O GLY D1048 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN D1053 " --> pdb=" O LYS D1049 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D1056 " --> pdb=" O GLY D1052 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA D1060 " --> pdb=" O LEU D1056 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS D1070 " --> pdb=" O ILE D1066 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1080 through 1089 removed outlier: 3.503A pdb=" N ARG D1086 " --> pdb=" O ILE D1082 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D1087 " --> pdb=" O SER D1083 " (cutoff:3.500A) Processing helix chain 'D' and resid 1114 through 1142 removed outlier: 4.279A pdb=" N ARG D1119 " --> pdb=" O LYS D1115 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS D1120 " --> pdb=" O GLU D1116 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG D1138 " --> pdb=" O LEU D1134 " (cutoff:3.500A) Processing helix chain 'D' and resid 1143 through 1164 removed outlier: 3.848A pdb=" N LEU D1157 " --> pdb=" O GLN D1153 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS D1164 " --> pdb=" O LYS D1160 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 93 removed outlier: 6.933A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 187 removed outlier: 3.582A pdb=" N VAL A 119 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A 118 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU A 276 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER A 120 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 262 Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 93 removed outlier: 6.933A pdb=" N ASN B 89 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU B 234 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU B 91 " --> pdb=" O LEU B 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 185 through 187 removed outlier: 3.582A pdb=" N VAL B 119 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 118 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B 276 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER B 120 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N CYS B 298 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TYR B 364 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 300 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 261 through 262 Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 93 removed outlier: 6.932A pdb=" N ASN C 89 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU C 234 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU C 91 " --> pdb=" O LEU C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 185 through 187 removed outlier: 3.582A pdb=" N VAL C 119 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL C 118 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU C 276 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER C 120 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LEU C 299 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU C 275 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL C 301 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU C 277 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS C 298 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TYR C 364 " --> pdb=" O CYS C 298 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU C 300 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 261 through 262 Processing sheet with id=AB1, first strand: chain 'D' and resid 89 through 93 removed outlier: 6.932A pdb=" N ASN D 89 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU D 234 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU D 91 " --> pdb=" O LEU D 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 185 through 187 removed outlier: 3.583A pdb=" N VAL D 119 " --> pdb=" O TRP D 152 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL D 118 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU D 276 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER D 120 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU D 299 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU D 275 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL D 301 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU D 277 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N CYS D 298 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR D 364 " --> pdb=" O CYS D 298 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU D 300 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 261 through 262 1510 hydrogen bonds defined for protein. 4470 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: 6.26 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4734 1.31 - 1.44: 8427 1.44 - 1.56: 17262 1.56 - 1.69: 145 1.69 - 1.82: 252 Bond restraints: 30820 Sorted by residual: bond pdb=" CAI Y01 B1302 " pdb=" CAZ Y01 B1302 " ideal model delta sigma weight residual 1.332 1.677 -0.345 2.00e-02 2.50e+03 2.97e+02 bond pdb=" CAI Y01 C1302 " pdb=" CAZ Y01 C1302 " ideal model delta sigma weight residual 1.332 1.677 -0.345 2.00e-02 2.50e+03 2.97e+02 bond pdb=" CAI Y01 D1302 " pdb=" CAZ Y01 D1302 " ideal model delta sigma weight residual 1.332 1.677 -0.345 2.00e-02 2.50e+03 2.97e+02 bond pdb=" CAI Y01 A1302 " pdb=" CAZ Y01 A1302 " ideal model delta sigma weight residual 1.332 1.676 -0.344 2.00e-02 2.50e+03 2.96e+02 bond pdb=" CAI Y01 C1301 " pdb=" CAZ Y01 C1301 " ideal model delta sigma weight residual 1.332 1.674 -0.342 2.00e-02 2.50e+03 2.93e+02 ... (remaining 30815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 39801 2.51 - 5.02: 1566 5.02 - 7.53: 338 7.53 - 10.03: 107 10.03 - 12.54: 24 Bond angle restraints: 41836 Sorted by residual: angle pdb=" N ILE B1165 " pdb=" CA ILE B1165 " pdb=" C ILE B1165 " ideal model delta sigma weight residual 113.10 108.06 5.04 9.70e-01 1.06e+00 2.70e+01 angle pdb=" N ILE A1165 " pdb=" CA ILE A1165 " pdb=" C ILE A1165 " ideal model delta sigma weight residual 113.10 108.08 5.02 9.70e-01 1.06e+00 2.68e+01 angle pdb=" N ILE D1165 " pdb=" CA ILE D1165 " pdb=" C ILE D1165 " ideal model delta sigma weight residual 113.10 108.08 5.02 9.70e-01 1.06e+00 2.67e+01 angle pdb=" N ILE C1165 " pdb=" CA ILE C1165 " pdb=" C ILE C1165 " ideal model delta sigma weight residual 113.10 108.09 5.01 9.70e-01 1.06e+00 2.67e+01 angle pdb=" CA TRP B 152 " pdb=" CB TRP B 152 " pdb=" CG TRP B 152 " ideal model delta sigma weight residual 113.60 123.16 -9.56 1.90e+00 2.77e-01 2.53e+01 ... (remaining 41831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 16508 16.00 - 32.01: 1178 32.01 - 48.01: 342 48.01 - 64.01: 32 64.01 - 80.02: 32 Dihedral angle restraints: 18092 sinusoidal: 7244 harmonic: 10848 Sorted by residual: dihedral pdb=" CA ALA A 392 " pdb=" C ALA A 392 " pdb=" N TYR A 393 " pdb=" CA TYR A 393 " ideal model delta harmonic sigma weight residual 180.00 -145.46 -34.54 0 5.00e+00 4.00e-02 4.77e+01 dihedral pdb=" CA ALA C 392 " pdb=" C ALA C 392 " pdb=" N TYR C 393 " pdb=" CA TYR C 393 " ideal model delta harmonic sigma weight residual -180.00 -145.46 -34.54 0 5.00e+00 4.00e-02 4.77e+01 dihedral pdb=" CA ALA D 392 " pdb=" C ALA D 392 " pdb=" N TYR D 393 " pdb=" CA TYR D 393 " ideal model delta harmonic sigma weight residual 180.00 -145.48 -34.52 0 5.00e+00 4.00e-02 4.77e+01 ... (remaining 18089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 4514 0.118 - 0.237: 166 0.237 - 0.355: 20 0.355 - 0.474: 12 0.474 - 0.592: 4 Chirality restraints: 4716 Sorted by residual: chirality pdb=" CBI Y01 C1303 " pdb=" CAU Y01 C1303 " pdb=" CBE Y01 C1303 " pdb=" CBG Y01 C1303 " both_signs ideal model delta sigma weight residual False 2.94 2.34 0.59 2.00e-01 2.50e+01 8.76e+00 chirality pdb=" CBI Y01 B1303 " pdb=" CAU Y01 B1303 " pdb=" CBE Y01 B1303 " pdb=" CBG Y01 B1303 " both_signs ideal model delta sigma weight residual False 2.94 2.35 0.59 2.00e-01 2.50e+01 8.71e+00 chirality pdb=" CBI Y01 D1303 " pdb=" CAU Y01 D1303 " pdb=" CBE Y01 D1303 " pdb=" CBG Y01 D1303 " both_signs ideal model delta sigma weight residual False 2.94 2.35 0.59 2.00e-01 2.50e+01 8.68e+00 ... (remaining 4713 not shown) Planarity restraints: 5252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 152 " -0.043 2.00e-02 2.50e+03 2.84e-02 2.01e+01 pdb=" CG TRP B 152 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP B 152 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 152 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 152 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 152 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 152 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 152 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 152 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 152 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 152 " 0.043 2.00e-02 2.50e+03 2.83e-02 2.01e+01 pdb=" CG TRP D 152 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP D 152 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP D 152 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP D 152 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 152 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 152 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 152 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 152 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 152 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 152 " -0.043 2.00e-02 2.50e+03 2.83e-02 2.01e+01 pdb=" CG TRP A 152 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP A 152 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 152 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 152 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 152 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 152 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 152 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 152 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 152 " -0.009 2.00e-02 2.50e+03 ... (remaining 5249 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 30 2.03 - 2.75: 4170 2.75 - 3.47: 43176 3.47 - 4.18: 73164 4.18 - 4.90: 125484 Nonbonded interactions: 246024 Sorted by model distance: nonbonded pdb=" CB TYR B 211 " pdb=" OH TYR B 227 " model vdw 1.313 3.440 nonbonded pdb=" CB TYR C 211 " pdb=" OH TYR C 227 " model vdw 1.313 3.440 nonbonded pdb=" CB TYR D 211 " pdb=" OH TYR D 227 " model vdw 1.314 3.440 nonbonded pdb=" CB TYR A 211 " pdb=" OH TYR A 227 " model vdw 1.314 3.440 nonbonded pdb=" O GLY C 157 " pdb=" OD1 ASP C 226 " model vdw 1.532 3.040 ... (remaining 246019 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 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: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.900 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 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 : 0.012 0.345 30824 Z= 0.588 Angle : 1.264 12.542 41844 Z= 0.658 Chirality : 0.065 0.592 4716 Planarity : 0.008 0.075 5252 Dihedral : 12.755 80.015 11088 Min Nonbonded Distance : 1.313 Molprobity Statistics. All-atom Clashscore : 26.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.66 % Favored : 90.13 % Rotamer: Outliers : 2.07 % Allowed : 8.42 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -5.81 (0.09), residues: 3728 helix: -3.71 (0.06), residues: 2352 sheet: -4.91 (0.20), residues: 216 loop : -3.39 (0.16), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 287 TYR 0.022 0.003 TYR A1063 PHE 0.030 0.003 PHE B 90 TRP 0.074 0.005 TRP A 152 HIS 0.008 0.001 HIS B 447 Details of bonding type rmsd/Z covalent geometry : bond 0.01207 / 0.59 (30820) covalent geometry : angle 1.26393 / 0.66 (41836) SS BOND : bond 0.01680 / 0.84 ( 4) SS BOND : angle 2.00778 / 1.03 ( 8) hydrogen bonds : bond 0.28335 / 19.38 ( 1510) hydrogen bonds : angle 10.10822 / 7.04 ( 4470) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1110 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.6846 (mt0) cc_final: 0.6434 (mp10) REVERT: A 172 ASP cc_start: 0.8148 (m-30) cc_final: 0.7766 (t0) REVERT: A 173 HIS cc_start: 0.8686 (t-90) cc_final: 0.8317 (t-170) REVERT: A 281 ASP cc_start: 0.7596 (m-30) cc_final: 0.7279 (p0) REVERT: A 284 MET cc_start: 0.6060 (tpp) cc_final: 0.5686 (tpp) REVERT: A 376 ILE cc_start: 0.9370 (mt) cc_final: 0.8960 (mt) REVERT: A 398 ARG cc_start: 0.7634 (ttt180) cc_final: 0.7431 (ttt180) REVERT: A 426 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7288 (tt0) REVERT: A 454 PHE cc_start: 0.8432 (t80) cc_final: 0.7822 (t80) REVERT: A 459 ARG cc_start: 0.8657 (mtp85) cc_final: 0.7571 (mtp85) REVERT: A 509 MET cc_start: 0.6856 (ttt) cc_final: 0.6314 (mmp) REVERT: A 577 TYR cc_start: 0.8558 (t80) cc_final: 0.8348 (t80) REVERT: A 590 LEU cc_start: 0.9352 (mm) cc_final: 0.9067 (mm) REVERT: A 615 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8773 (tp) REVERT: A 679 LYS cc_start: 0.9214 (mmpt) cc_final: 0.9009 (mmtm) REVERT: A 800 VAL cc_start: 0.9009 (p) cc_final: 0.8671 (p) REVERT: A 813 LEU cc_start: 0.8922 (mt) cc_final: 0.8606 (mt) REVERT: A 814 GLU cc_start: 0.7618 (tp30) cc_final: 0.7388 (tp30) REVERT: A 831 GLN cc_start: 0.8371 (tt0) cc_final: 0.8162 (tt0) REVERT: A 1044 SER cc_start: 0.8788 (m) cc_final: 0.8588 (m) REVERT: A 1129 LYS cc_start: 0.8756 (ttpt) cc_final: 0.7860 (ptmm) REVERT: A 1140 LYS cc_start: 0.9157 (ttmm) cc_final: 0.8867 (tptp) REVERT: A 1161 GLN cc_start: 0.9084 (mm110) cc_final: 0.8549 (mt0) REVERT: B 420 TRP cc_start: 0.5789 (m100) cc_final: 0.5327 (m100) REVERT: B 426 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7119 (tp30) REVERT: B 454 PHE cc_start: 0.8299 (t80) cc_final: 0.8093 (t80) REVERT: B 459 ARG cc_start: 0.8649 (mtp85) cc_final: 0.7875 (mtp180) REVERT: B 505 HIS cc_start: 0.6667 (t70) cc_final: 0.6442 (t-170) REVERT: B 608 GLU cc_start: 0.7942 (tp30) cc_final: 0.7414 (tp30) REVERT: B 622 MET cc_start: 0.8392 (ttp) cc_final: 0.8127 (ttp) REVERT: B 625 ASP cc_start: 0.8360 (m-30) cc_final: 0.8022 (m-30) REVERT: B 865 ASN cc_start: 0.8571 (m-40) cc_final: 0.8364 (m-40) REVERT: B 879 VAL cc_start: 0.8966 (t) cc_final: 0.8736 (t) REVERT: B 980 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8103 (mt0) REVERT: B 1015 TYR cc_start: 0.8618 (t80) cc_final: 0.8375 (t80) REVERT: B 1129 LYS cc_start: 0.8460 (ttpt) cc_final: 0.8120 (ttpt) REVERT: B 1140 LYS cc_start: 0.9062 (ttmm) cc_final: 0.8531 (ttmm) REVERT: B 1160 LYS cc_start: 0.8996 (mmtp) cc_final: 0.7973 (tptp) REVERT: C 155 THR cc_start: 0.7707 (p) cc_final: 0.7308 (t) REVERT: C 355 MET cc_start: 0.5240 (tpp) cc_final: 0.4984 (tpt) REVERT: C 383 LYS cc_start: 0.7755 (mtpt) cc_final: 0.7344 (tttm) REVERT: C 420 TRP cc_start: 0.5860 (m100) cc_final: 0.5309 (m100) REVERT: C 426 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7029 (tp30) REVERT: C 454 PHE cc_start: 0.8364 (t80) cc_final: 0.7769 (t80) REVERT: C 509 MET cc_start: 0.6574 (ttt) cc_final: 0.6027 (mmp) REVERT: C 578 PHE cc_start: 0.9123 (m-10) cc_final: 0.8716 (m-80) REVERT: C 601 ARG cc_start: 0.8241 (mtp-110) cc_final: 0.7861 (mtt180) REVERT: C 625 ASP cc_start: 0.8348 (m-30) cc_final: 0.8118 (m-30) REVERT: C 626 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9294 (tp) REVERT: C 804 ASP cc_start: 0.7065 (t0) cc_final: 0.6645 (t0) REVERT: C 879 VAL cc_start: 0.8944 (t) cc_final: 0.8553 (t) REVERT: C 1067 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7876 (ttt90) REVERT: C 1125 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8350 (tm-30) REVERT: C 1140 LYS cc_start: 0.9136 (ttmm) cc_final: 0.8658 (ttmm) REVERT: C 1160 LYS cc_start: 0.8922 (mmtp) cc_final: 0.8479 (mmtp) REVERT: D 355 MET cc_start: 0.4820 (tpp) cc_final: 0.4585 (tpt) REVERT: D 383 LYS cc_start: 0.7640 (mtpt) cc_final: 0.7277 (tttm) REVERT: D 420 TRP cc_start: 0.5816 (m100) cc_final: 0.5200 (m100) REVERT: D 426 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6923 (tp30) REVERT: D 454 PHE cc_start: 0.8244 (t80) cc_final: 0.6939 (t80) REVERT: D 459 ARG cc_start: 0.8479 (mtp85) cc_final: 0.7060 (mtp85) REVERT: D 509 MET cc_start: 0.6483 (ttt) cc_final: 0.5897 (mmp) REVERT: D 578 PHE cc_start: 0.9077 (m-10) cc_final: 0.8839 (m-80) REVERT: D 601 ARG cc_start: 0.8174 (mtp-110) cc_final: 0.7898 (mtt180) REVERT: D 608 GLU cc_start: 0.7749 (tp30) cc_final: 0.7542 (tp30) REVERT: D 625 ASP cc_start: 0.8294 (m-30) cc_final: 0.7913 (m-30) REVERT: D 804 ASP cc_start: 0.7083 (t0) cc_final: 0.6655 (t0) REVERT: D 879 VAL cc_start: 0.8944 (t) cc_final: 0.8553 (t) REVERT: D 892 ARG cc_start: 0.8167 (ttt180) cc_final: 0.7746 (ttt-90) REVERT: D 980 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8025 (mt0) REVERT: D 1015 TYR cc_start: 0.8680 (t80) cc_final: 0.8441 (t80) REVERT: D 1045 TYR cc_start: 0.8345 (t80) cc_final: 0.8089 (t80) REVERT: D 1067 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7852 (ttt90) REVERT: D 1125 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8247 (tm-30) REVERT: D 1129 LYS cc_start: 0.8478 (ttpt) cc_final: 0.8009 (ttmt) REVERT: D 1140 LYS cc_start: 0.9091 (ttmm) cc_final: 0.8683 (ttmm) REVERT: D 1160 LYS cc_start: 0.8925 (mmtp) cc_final: 0.8156 (mmtp) outliers start: 64 outliers final: 16 residues processed: 1152 average time/residue: 0.2089 time to fit residues: 368.9575 Evaluate side-chains 764 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 744 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 914 LYS Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 914 LYS Chi-restraints excluded: chain C residue 980 GLN Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 914 LYS Chi-restraints excluded: chain D residue 980 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN A 173 HIS A 228 ASN A 348 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 673 GLN A 774 HIS A 786 ASN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN A1153 GLN A1161 GLN B 116 ASN B 174 GLN ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN B 348 GLN B 447 HIS B 462 GLN B 570 ASN B 673 GLN B 774 HIS B 786 ASN B 889 HIS B1037 ASN B1070 HIS ** B1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1131 ASN C 116 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 GLN C 228 ASN C 462 GLN C 660 GLN C 673 GLN C 774 HIS C 786 ASN C 980 GLN ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN C1108 HIS C1131 ASN D 116 ASN D 147 GLN ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 GLN D 462 GLN D 570 ASN D 673 GLN D 774 HIS D 786 ASN D1037 ASN D1108 HIS D1131 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.183345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.133001 restraints weight = 47202.894| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.67 r_work: 0.3417 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30824 Z= 0.178 Angle : 0.769 9.875 41844 Z= 0.378 Chirality : 0.042 0.227 4716 Planarity : 0.007 0.070 5252 Dihedral : 8.004 89.481 4351 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.37 % Allowed : 16.00 % Favored : 79.63 % 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: -3.45 (0.12), residues: 3728 helix: -1.58 (0.09), residues: 2388 sheet: -4.55 (0.22), residues: 192 loop : -3.12 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 611 TYR 0.019 0.002 TYR D 888 PHE 0.022 0.002 PHE D 899 TRP 0.025 0.003 TRP C 820 HIS 0.015 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 (30820) covalent geometry : angle 0.76937 / 0.38 (41836) SS BOND : bond 0.00083 / 0.04 ( 4) SS BOND : angle 0.56574 / 0.30 ( 8) hydrogen bonds : bond 0.04638 / 3.20 ( 1510) hydrogen bonds : angle 4.99274 / 3.47 ( 4470) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 880 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7116 (tt) REVERT: A 173 HIS cc_start: 0.8687 (t70) cc_final: 0.8399 (t70) REVERT: A 186 MET cc_start: 0.8056 (mpt) cc_final: 0.7781 (mpt) REVERT: A 281 ASP cc_start: 0.8046 (m-30) cc_final: 0.7377 (p0) REVERT: A 284 MET cc_start: 0.6027 (tpp) cc_final: 0.5519 (ttp) REVERT: A 413 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8377 (mt) REVERT: A 454 PHE cc_start: 0.7989 (t80) cc_final: 0.7780 (t80) REVERT: A 462 GLN cc_start: 0.8894 (mt0) cc_final: 0.8661 (mt0) REVERT: A 509 MET cc_start: 0.6631 (ttt) cc_final: 0.5925 (mmp) REVERT: A 563 LEU cc_start: 0.9205 (tp) cc_final: 0.8946 (tp) REVERT: A 601 ARG cc_start: 0.8667 (mtp-110) cc_final: 0.8438 (ptm160) REVERT: A 629 GLU cc_start: 0.8749 (tt0) cc_final: 0.8390 (tt0) REVERT: A 660 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8122 (mp-120) REVERT: A 694 VAL cc_start: 0.9370 (t) cc_final: 0.9151 (m) REVERT: A 786 ASN cc_start: 0.9084 (m-40) cc_final: 0.8847 (m-40) REVERT: A 804 ASP cc_start: 0.7529 (t0) cc_final: 0.7286 (t0) REVERT: A 827 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7965 (mm-30) REVERT: A 857 ARG cc_start: 0.7191 (ttm110) cc_final: 0.6791 (ptp-110) REVERT: A 866 GLN cc_start: 0.8501 (mt0) cc_final: 0.8289 (mt0) REVERT: A 867 CYS cc_start: 0.7522 (m) cc_final: 0.7285 (t) REVERT: A 1029 LEU cc_start: 0.9458 (tp) cc_final: 0.9167 (tp) REVERT: A 1067 ARG cc_start: 0.8617 (tmm-80) cc_final: 0.7895 (ttt90) REVERT: A 1080 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7582 (tt) REVERT: A 1138 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8220 (ttm110) REVERT: A 1161 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8687 (mt0) REVERT: B 259 GLN cc_start: 0.6685 (mm110) cc_final: 0.6479 (mt0) REVERT: B 316 GLU cc_start: 0.7809 (mp0) cc_final: 0.7596 (mp0) REVERT: B 584 ASN cc_start: 0.8778 (m-40) cc_final: 0.8531 (m-40) REVERT: B 595 LEU cc_start: 0.9194 (mp) cc_final: 0.8899 (mp) REVERT: B 601 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7483 (mtt180) REVERT: B 629 GLU cc_start: 0.8697 (tt0) cc_final: 0.8185 (tt0) REVERT: B 656 GLN cc_start: 0.8729 (mt0) cc_final: 0.7913 (mt0) REVERT: B 660 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7957 (mp-120) REVERT: B 710 PHE cc_start: 0.8613 (m-80) cc_final: 0.8325 (m-80) REVERT: B 828 GLU cc_start: 0.8138 (tp30) cc_final: 0.7429 (tm-30) REVERT: B 865 ASN cc_start: 0.8885 (m-40) cc_final: 0.8147 (m-40) REVERT: B 1064 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8295 (ttm110) REVERT: B 1067 ARG cc_start: 0.8562 (tmm-80) cc_final: 0.7897 (ttt90) REVERT: B 1080 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7243 (tt) REVERT: B 1130 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8562 (mt-10) REVERT: B 1160 LYS cc_start: 0.9037 (mmtp) cc_final: 0.8826 (tmmt) REVERT: C 173 HIS cc_start: 0.8827 (t-170) cc_final: 0.8347 (t-170) REVERT: C 509 MET cc_start: 0.6398 (ttt) cc_final: 0.5803 (mmp) REVERT: C 570 ASN cc_start: 0.9168 (t0) cc_final: 0.8776 (t0) REVERT: C 595 LEU cc_start: 0.9103 (mp) cc_final: 0.8795 (mp) REVERT: C 601 ARG cc_start: 0.8666 (mtp-110) cc_final: 0.7849 (mtt180) REVERT: C 615 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8884 (tp) REVERT: C 629 GLU cc_start: 0.8606 (tt0) cc_final: 0.8127 (tt0) REVERT: C 699 CYS cc_start: 0.7836 (m) cc_final: 0.7585 (t) REVERT: C 710 PHE cc_start: 0.8455 (m-80) cc_final: 0.8197 (m-80) REVERT: C 776 TRP cc_start: 0.8273 (m100) cc_final: 0.7657 (m100) REVERT: C 784 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8803 (ttp) REVERT: C 804 ASP cc_start: 0.7469 (t0) cc_final: 0.6909 (t0) REVERT: C 866 GLN cc_start: 0.8529 (mt0) cc_final: 0.8294 (mt0) REVERT: C 879 VAL cc_start: 0.8846 (t) cc_final: 0.8577 (t) REVERT: C 892 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.8130 (ttm-80) REVERT: C 1067 ARG cc_start: 0.8621 (ttp80) cc_final: 0.8038 (ttt90) REVERT: C 1080 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7626 (mt) REVERT: C 1160 LYS cc_start: 0.9016 (mmtp) cc_final: 0.8767 (mmtp) REVERT: D 113 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7944 (ttp80) REVERT: D 175 MET cc_start: 0.7688 (ptm) cc_final: 0.7369 (ppp) REVERT: D 454 PHE cc_start: 0.7778 (t80) cc_final: 0.7432 (t80) REVERT: D 509 MET cc_start: 0.6432 (ttt) cc_final: 0.5712 (mmp) REVERT: D 594 LEU cc_start: 0.9544 (tp) cc_final: 0.9231 (tp) REVERT: D 601 ARG cc_start: 0.8626 (mtp-110) cc_final: 0.7860 (mtt180) REVERT: D 629 GLU cc_start: 0.8695 (tt0) cc_final: 0.8132 (tt0) REVERT: D 656 GLN cc_start: 0.8727 (mt0) cc_final: 0.8058 (mt0) REVERT: D 660 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7795 (mp-120) REVERT: D 710 PHE cc_start: 0.8567 (m-80) cc_final: 0.8324 (m-80) REVERT: D 815 LEU cc_start: 0.8998 (mt) cc_final: 0.8769 (mt) REVERT: D 827 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7840 (mm-30) REVERT: D 892 ARG cc_start: 0.8389 (ttt180) cc_final: 0.8178 (ttt90) REVERT: D 1067 ARG cc_start: 0.8620 (ttp80) cc_final: 0.8013 (ttt90) REVERT: D 1080 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7517 (mt) REVERT: D 1160 LYS cc_start: 0.9035 (mmtp) cc_final: 0.8773 (mmtp) outliers start: 135 outliers final: 51 residues processed: 960 average time/residue: 0.1880 time to fit residues: 284.2206 Evaluate side-chains 790 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 725 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 570 ASN Chi-restraints excluded: chain B residue 601 ARG Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 660 GLN Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 914 LYS Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 914 LYS Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 914 LYS Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1121 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 207 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 270 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 293 optimal weight: 7.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 GLN A 404 ASN A 570 ASN A 573 GLN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 GLN A1161 GLN B 228 ASN B 295 GLN B 570 ASN B 573 GLN B 786 ASN B1070 HIS C 165 HIS ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 GLN C 573 GLN C 786 ASN C1017 ASN C1084 HIS ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN D 228 ASN D 348 GLN D 573 GLN D 786 ASN D 866 GLN D1017 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.177326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.124415 restraints weight = 47378.585| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.59 r_work: 0.3345 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30824 Z= 0.197 Angle : 0.745 11.252 41844 Z= 0.363 Chirality : 0.043 0.260 4716 Planarity : 0.006 0.066 5252 Dihedral : 7.035 59.686 4326 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.53 % Favored : 91.36 % Rotamer: Outliers : 5.15 % Allowed : 19.49 % Favored : 75.36 % 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: -2.09 (0.13), residues: 3728 helix: -0.30 (0.10), residues: 2364 sheet: -4.26 (0.26), residues: 192 loop : -3.03 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 398 TYR 0.016 0.002 TYR B1063 PHE 0.031 0.002 PHE B1069 TRP 0.025 0.002 TRP A 152 HIS 0.023 0.001 HIS B1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (30820) covalent geometry : angle 0.74538 / 0.36 (41836) SS BOND : bond 0.00052 / 0.03 ( 4) SS BOND : angle 0.69624 / 0.37 ( 8) hydrogen bonds : bond 0.04155 / 2.88 ( 1510) hydrogen bonds : angle 4.57555 / 3.17 ( 4470) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 812 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 HIS cc_start: 0.8769 (t70) cc_final: 0.8315 (t-170) REVERT: A 175 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7475 (ppp) REVERT: A 186 MET cc_start: 0.8075 (mpt) cc_final: 0.7648 (mpt) REVERT: A 281 ASP cc_start: 0.7981 (m-30) cc_final: 0.7354 (p0) REVERT: A 284 MET cc_start: 0.6048 (tpp) cc_final: 0.5533 (ttp) REVERT: A 358 LYS cc_start: 0.5959 (OUTLIER) cc_final: 0.5669 (ttmt) REVERT: A 431 ASP cc_start: 0.9201 (m-30) cc_final: 0.8945 (m-30) REVERT: A 509 MET cc_start: 0.6557 (ttt) cc_final: 0.5809 (mmp) REVERT: A 590 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9097 (mm) REVERT: A 601 ARG cc_start: 0.8500 (mtp-110) cc_final: 0.8245 (ptm160) REVERT: A 629 GLU cc_start: 0.8850 (tt0) cc_final: 0.8435 (tt0) REVERT: A 660 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8190 (mp-120) REVERT: A 776 TRP cc_start: 0.8527 (m100) cc_final: 0.8293 (m100) REVERT: A 804 ASP cc_start: 0.7702 (t0) cc_final: 0.7482 (t0) REVERT: A 813 LEU cc_start: 0.8797 (mt) cc_final: 0.8542 (mt) REVERT: A 857 ARG cc_start: 0.7076 (ttm110) cc_final: 0.6669 (ptp-110) REVERT: A 867 CYS cc_start: 0.7671 (m) cc_final: 0.7372 (t) REVERT: A 1029 LEU cc_start: 0.9512 (tp) cc_final: 0.9161 (tp) REVERT: A 1067 ARG cc_start: 0.8662 (tmm-80) cc_final: 0.8113 (ttt90) REVERT: A 1080 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7492 (tt) REVERT: A 1138 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8198 (ttm110) REVERT: A 1161 GLN cc_start: 0.8882 (mm110) cc_final: 0.8577 (mt0) REVERT: B 186 MET cc_start: 0.8491 (mpt) cc_final: 0.7991 (mpt) REVERT: B 259 GLN cc_start: 0.6650 (mm110) cc_final: 0.6342 (mt0) REVERT: B 372 GLU cc_start: 0.8406 (mp0) cc_final: 0.8028 (pm20) REVERT: B 397 LEU cc_start: 0.9338 (tt) cc_final: 0.9083 (pt) REVERT: B 431 ASP cc_start: 0.9045 (m-30) cc_final: 0.8827 (m-30) REVERT: B 509 MET cc_start: 0.6594 (ttt) cc_final: 0.5819 (mmp) REVERT: B 595 LEU cc_start: 0.9338 (mp) cc_final: 0.9137 (mp) REVERT: B 601 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7488 (mtt180) REVERT: B 629 GLU cc_start: 0.8718 (tt0) cc_final: 0.8266 (tt0) REVERT: B 656 GLN cc_start: 0.8846 (mt0) cc_final: 0.7955 (mt0) REVERT: B 660 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8142 (mp-120) REVERT: B 767 ARG cc_start: 0.7365 (tmm160) cc_final: 0.7112 (tmm160) REVERT: B 819 PHE cc_start: 0.8819 (t80) cc_final: 0.8567 (t80) REVERT: B 827 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7885 (tp30) REVERT: B 828 GLU cc_start: 0.8151 (tp30) cc_final: 0.7320 (tm-30) REVERT: B 865 ASN cc_start: 0.8905 (m-40) cc_final: 0.8616 (m-40) REVERT: B 892 ARG cc_start: 0.8530 (ttm-80) cc_final: 0.8326 (ttm-80) REVERT: B 1067 ARG cc_start: 0.8675 (tmm-80) cc_final: 0.8105 (ttt90) REVERT: B 1080 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7643 (tt) REVERT: B 1118 GLU cc_start: 0.8314 (tt0) cc_final: 0.8087 (tp30) REVERT: C 173 HIS cc_start: 0.8769 (t-170) cc_final: 0.8349 (t-170) REVERT: C 186 MET cc_start: 0.8493 (mpt) cc_final: 0.8091 (mpt) REVERT: C 431 ASP cc_start: 0.9004 (m-30) cc_final: 0.8773 (m-30) REVERT: C 436 ASP cc_start: 0.8320 (t70) cc_final: 0.8092 (t70) REVERT: C 509 MET cc_start: 0.6460 (ttt) cc_final: 0.5770 (mmp) REVERT: C 595 LEU cc_start: 0.9305 (mp) cc_final: 0.9091 (mp) REVERT: C 601 ARG cc_start: 0.8679 (mtp-110) cc_final: 0.8313 (ptm160) REVERT: C 622 MET cc_start: 0.8928 (ttp) cc_final: 0.8559 (ttp) REVERT: C 629 GLU cc_start: 0.8652 (tt0) cc_final: 0.8259 (tt0) REVERT: C 660 GLN cc_start: 0.8825 (mp10) cc_final: 0.8203 (mt0) REVERT: C 784 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8773 (ttp) REVERT: C 795 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8772 (tp) REVERT: C 804 ASP cc_start: 0.7602 (t0) cc_final: 0.7251 (t0) REVERT: C 827 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7743 (tp30) REVERT: C 857 ARG cc_start: 0.6946 (ttm110) cc_final: 0.6521 (ptp-110) REVERT: C 867 CYS cc_start: 0.7745 (m) cc_final: 0.7496 (t) REVERT: C 1067 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8186 (ttt90) REVERT: C 1160 LYS cc_start: 0.9029 (mmtp) cc_final: 0.8798 (mmtp) REVERT: D 113 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7789 (ttp80) REVERT: D 186 MET cc_start: 0.8243 (mpt) cc_final: 0.7982 (mpt) REVERT: D 431 ASP cc_start: 0.8929 (m-30) cc_final: 0.8702 (m-30) REVERT: D 509 MET cc_start: 0.6507 (ttt) cc_final: 0.5692 (mmp) REVERT: D 594 LEU cc_start: 0.9542 (tp) cc_final: 0.9273 (tp) REVERT: D 595 LEU cc_start: 0.9325 (mp) cc_final: 0.9102 (mp) REVERT: D 601 ARG cc_start: 0.8665 (mtp-110) cc_final: 0.8430 (ptm160) REVERT: D 629 GLU cc_start: 0.8684 (tt0) cc_final: 0.8128 (tt0) REVERT: D 767 ARG cc_start: 0.7370 (tmm160) cc_final: 0.7134 (tmm160) REVERT: D 804 ASP cc_start: 0.7474 (t0) cc_final: 0.7246 (t0) REVERT: D 819 PHE cc_start: 0.8889 (t80) cc_final: 0.8494 (t80) REVERT: D 873 THR cc_start: 0.8661 (t) cc_final: 0.8414 (t) REVERT: D 882 ARG cc_start: 0.8898 (ttp80) cc_final: 0.8502 (ttp80) REVERT: D 892 ARG cc_start: 0.8449 (ttt180) cc_final: 0.8117 (ttt90) REVERT: D 1067 ARG cc_start: 0.8589 (ttp80) cc_final: 0.8143 (ttt90) REVERT: D 1080 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7466 (tt) REVERT: D 1160 LYS cc_start: 0.9018 (mmtp) cc_final: 0.8807 (mmtp) outliers start: 159 outliers final: 78 residues processed: 894 average time/residue: 0.1838 time to fit residues: 260.7160 Evaluate side-chains 816 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 725 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 601 ARG Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 660 GLN Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 874 CYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 863 SER Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1121 LEU Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 210 optimal weight: 4.9990 chunk 79 optimal weight: 0.3980 chunk 312 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 219 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 329 optimal weight: 0.6980 chunk 332 optimal weight: 10.0000 chunk 319 optimal weight: 0.4980 chunk 144 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 573 GLN A 786 ASN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN B 786 ASN B1070 HIS ** B1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 HIS C 573 GLN ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 462 GLN D 573 GLN D 786 ASN D 866 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.175575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.122653 restraints weight = 46942.059| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.59 r_work: 0.3320 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 30824 Z= 0.186 Angle : 0.727 10.725 41844 Z= 0.349 Chirality : 0.042 0.173 4716 Planarity : 0.005 0.069 5252 Dihedral : 6.581 58.768 4308 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.40 % Favored : 91.50 % Rotamer: Outliers : 4.79 % Allowed : 20.66 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.14), residues: 3728 helix: 0.22 (0.10), residues: 2388 sheet: -3.87 (0.31), residues: 184 loop : -2.87 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1064 TYR 0.024 0.002 TYR A 859 PHE 0.030 0.002 PHE B 454 TRP 0.024 0.002 TRP A 133 HIS 0.019 0.001 HIS B1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (30820) covalent geometry : angle 0.72680 / 0.35 (41836) SS BOND : bond 0.00067 / 0.03 ( 4) SS BOND : angle 0.70127 / 0.37 ( 8) hydrogen bonds : bond 0.03933 / 2.71 ( 1510) hydrogen bonds : angle 4.39409 / 3.04 ( 4470) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 791 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 HIS cc_start: 0.8739 (t70) cc_final: 0.8536 (t-170) REVERT: A 186 MET cc_start: 0.8008 (mpt) cc_final: 0.7580 (mpt) REVERT: A 281 ASP cc_start: 0.8001 (m-30) cc_final: 0.7468 (p0) REVERT: A 284 MET cc_start: 0.5782 (tpp) cc_final: 0.5447 (ttp) REVERT: A 358 LYS cc_start: 0.6008 (OUTLIER) cc_final: 0.5743 (ttmt) REVERT: A 413 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8311 (mt) REVERT: A 431 ASP cc_start: 0.9199 (m-30) cc_final: 0.8940 (m-30) REVERT: A 447 HIS cc_start: 0.8473 (t70) cc_final: 0.8233 (t70) REVERT: A 509 MET cc_start: 0.6611 (ttt) cc_final: 0.5870 (mmp) REVERT: A 601 ARG cc_start: 0.8411 (mtp-110) cc_final: 0.8203 (ptm160) REVERT: A 629 GLU cc_start: 0.8853 (tt0) cc_final: 0.8362 (tt0) REVERT: A 644 ARG cc_start: 0.8438 (ptm-80) cc_final: 0.8108 (ptm-80) REVERT: A 656 GLN cc_start: 0.8805 (mt0) cc_final: 0.8195 (mt0) REVERT: A 660 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8220 (mp-120) REVERT: A 776 TRP cc_start: 0.8542 (m100) cc_final: 0.8262 (m100) REVERT: A 804 ASP cc_start: 0.7625 (t0) cc_final: 0.7413 (t0) REVERT: A 813 LEU cc_start: 0.8764 (mt) cc_final: 0.8497 (mt) REVERT: A 827 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7951 (tp30) REVERT: A 857 ARG cc_start: 0.6974 (ttm110) cc_final: 0.6531 (ptp-110) REVERT: A 867 CYS cc_start: 0.7828 (m) cc_final: 0.7504 (t) REVERT: A 952 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9031 (pt) REVERT: A 1029 LEU cc_start: 0.9545 (tp) cc_final: 0.9189 (tp) REVERT: A 1038 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9229 (tp) REVERT: A 1067 ARG cc_start: 0.8592 (tmm-80) cc_final: 0.8119 (ttt90) REVERT: A 1080 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7647 (tt) REVERT: A 1138 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8264 (ttm110) REVERT: B 186 MET cc_start: 0.8384 (mpt) cc_final: 0.7862 (mpt) REVERT: B 259 GLN cc_start: 0.6715 (mm110) cc_final: 0.6306 (mt0) REVERT: B 372 GLU cc_start: 0.8447 (mp0) cc_final: 0.8154 (pm20) REVERT: B 397 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9047 (pp) REVERT: B 431 ASP cc_start: 0.9023 (m-30) cc_final: 0.8745 (m-30) REVERT: B 472 LEU cc_start: 0.8434 (tt) cc_final: 0.7989 (mt) REVERT: B 509 MET cc_start: 0.6757 (ttt) cc_final: 0.5945 (mmp) REVERT: B 595 LEU cc_start: 0.9378 (mp) cc_final: 0.9143 (mp) REVERT: B 629 GLU cc_start: 0.8695 (tt0) cc_final: 0.8298 (tt0) REVERT: B 633 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8591 (p) REVERT: B 827 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7728 (tp30) REVERT: B 882 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8604 (ttp80) REVERT: B 892 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.8319 (ttm-80) REVERT: B 1067 ARG cc_start: 0.8615 (tmm-80) cc_final: 0.8119 (ttt90) REVERT: B 1080 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7659 (tt) REVERT: C 173 HIS cc_start: 0.8770 (t-170) cc_final: 0.8376 (t-170) REVERT: C 186 MET cc_start: 0.8426 (mpt) cc_final: 0.8006 (mpt) REVERT: C 249 PHE cc_start: 0.8190 (t80) cc_final: 0.7894 (t80) REVERT: C 431 ASP cc_start: 0.9057 (m-30) cc_final: 0.8804 (m-30) REVERT: C 509 MET cc_start: 0.6602 (ttt) cc_final: 0.5733 (mmp) REVERT: C 601 ARG cc_start: 0.8658 (mtp-110) cc_final: 0.8335 (ptm160) REVERT: C 608 GLU cc_start: 0.8668 (tp30) cc_final: 0.7946 (tp30) REVERT: C 611 ARG cc_start: 0.8796 (ttm110) cc_final: 0.8531 (ttp80) REVERT: C 629 GLU cc_start: 0.8673 (tt0) cc_final: 0.8294 (tt0) REVERT: C 784 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8781 (ttp) REVERT: C 795 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8750 (tp) REVERT: C 804 ASP cc_start: 0.7605 (t0) cc_final: 0.7298 (t0) REVERT: C 819 PHE cc_start: 0.8952 (t80) cc_final: 0.8559 (t80) REVERT: C 827 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7543 (tp30) REVERT: C 857 ARG cc_start: 0.6969 (ttm110) cc_final: 0.6515 (ptp-110) REVERT: C 867 CYS cc_start: 0.7775 (m) cc_final: 0.7541 (t) REVERT: C 892 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.7969 (ttt-90) REVERT: C 952 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9016 (pt) REVERT: C 1067 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8180 (ttt90) REVERT: C 1080 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7811 (tt) REVERT: C 1160 LYS cc_start: 0.9011 (mmtp) cc_final: 0.8791 (mmtp) REVERT: D 113 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7888 (ttp80) REVERT: D 186 MET cc_start: 0.8359 (mpt) cc_final: 0.7961 (mpt) REVERT: D 259 GLN cc_start: 0.6549 (mm110) cc_final: 0.6259 (mt0) REVERT: D 431 ASP cc_start: 0.8990 (m-30) cc_final: 0.8736 (m-30) REVERT: D 509 MET cc_start: 0.6607 (ttt) cc_final: 0.5693 (mmp) REVERT: D 601 ARG cc_start: 0.8706 (mtp-110) cc_final: 0.8456 (ptm160) REVERT: D 622 MET cc_start: 0.8894 (ttp) cc_final: 0.8346 (ttp) REVERT: D 629 GLU cc_start: 0.8645 (tt0) cc_final: 0.8207 (tt0) REVERT: D 656 GLN cc_start: 0.8853 (mt0) cc_final: 0.8115 (mt0) REVERT: D 660 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8113 (mp-120) REVERT: D 795 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8867 (tp) REVERT: D 804 ASP cc_start: 0.7442 (t0) cc_final: 0.7076 (t0) REVERT: D 813 LEU cc_start: 0.8734 (mt) cc_final: 0.8469 (mt) REVERT: D 819 PHE cc_start: 0.8927 (t80) cc_final: 0.8484 (t80) REVERT: D 827 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7736 (tp30) REVERT: D 828 GLU cc_start: 0.8115 (tp30) cc_final: 0.7819 (tp30) REVERT: D 882 ARG cc_start: 0.8852 (ttp80) cc_final: 0.8590 (ttp80) REVERT: D 892 ARG cc_start: 0.8400 (ttt180) cc_final: 0.8138 (ttt90) REVERT: D 952 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8977 (pt) REVERT: D 1067 ARG cc_start: 0.8580 (ttp80) cc_final: 0.8157 (ttt90) REVERT: D 1080 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7808 (tt) outliers start: 148 outliers final: 80 residues processed: 874 average time/residue: 0.1894 time to fit residues: 263.4073 Evaluate side-chains 822 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 723 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 874 CYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain C residue 1121 LEU Chi-restraints excluded: chain C residue 1134 LEU Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 303 optimal weight: 0.9990 chunk 350 optimal weight: 0.9980 chunk 268 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 224 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 ASN A 573 GLN A 786 ASN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN B1070 HIS B1108 HIS C 573 GLN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.177244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.125945 restraints weight = 47250.488| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.80 r_work: 0.3330 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30824 Z= 0.146 Angle : 0.682 11.051 41844 Z= 0.327 Chirality : 0.041 0.172 4716 Planarity : 0.005 0.063 5252 Dihedral : 6.255 59.614 4308 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.97 % Favored : 91.93 % Rotamer: Outliers : 4.89 % Allowed : 21.53 % Favored : 73.58 % 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: -0.98 (0.14), residues: 3728 helix: 0.60 (0.11), residues: 2392 sheet: -3.72 (0.33), residues: 184 loop : -2.81 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 171 TYR 0.016 0.001 TYR A 859 PHE 0.024 0.002 PHE B 454 TRP 0.019 0.002 TRP B 680 HIS 0.018 0.001 HIS B1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (30820) covalent geometry : angle 0.68159 / 0.33 (41836) SS BOND : bond 0.00045 / 0.02 ( 4) SS BOND : angle 0.49159 / 0.26 ( 8) hydrogen bonds : bond 0.03697 / 2.54 ( 1510) hydrogen bonds : angle 4.22243 / 2.92 ( 4470) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 821 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.5600 (mp10) cc_final: 0.5390 (mp10) REVERT: A 173 HIS cc_start: 0.8741 (t70) cc_final: 0.8523 (t-170) REVERT: A 186 MET cc_start: 0.8009 (mpt) cc_final: 0.7491 (mpt) REVERT: A 260 GLN cc_start: 0.7931 (mm110) cc_final: 0.7670 (mm110) REVERT: A 281 ASP cc_start: 0.8045 (m-30) cc_final: 0.7597 (p0) REVERT: A 284 MET cc_start: 0.5924 (tpp) cc_final: 0.5461 (ttp) REVERT: A 358 LYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5795 (ttmt) REVERT: A 413 LEU cc_start: 0.9001 (tt) cc_final: 0.8711 (mm) REVERT: A 431 ASP cc_start: 0.9155 (m-30) cc_final: 0.8882 (m-30) REVERT: A 447 HIS cc_start: 0.8543 (t70) cc_final: 0.8278 (t70) REVERT: A 454 PHE cc_start: 0.6941 (t80) cc_final: 0.6630 (t80) REVERT: A 509 MET cc_start: 0.6788 (ttt) cc_final: 0.5990 (mmp) REVERT: A 611 ARG cc_start: 0.8817 (ttp80) cc_final: 0.8605 (ttp80) REVERT: A 629 GLU cc_start: 0.8917 (tt0) cc_final: 0.8498 (tt0) REVERT: A 804 ASP cc_start: 0.7479 (t0) cc_final: 0.7179 (t0) REVERT: A 813 LEU cc_start: 0.8763 (mt) cc_final: 0.8525 (mt) REVERT: A 827 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7725 (tp30) REVERT: A 828 GLU cc_start: 0.8280 (tp30) cc_final: 0.7941 (tp30) REVERT: A 857 ARG cc_start: 0.6905 (ttm110) cc_final: 0.6467 (ptp-110) REVERT: A 867 CYS cc_start: 0.7806 (m) cc_final: 0.7290 (t) REVERT: A 952 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9048 (pt) REVERT: A 988 MET cc_start: 0.8746 (mtt) cc_final: 0.8413 (mtm) REVERT: A 1029 LEU cc_start: 0.9556 (tp) cc_final: 0.9166 (tp) REVERT: A 1038 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9227 (tp) REVERT: A 1067 ARG cc_start: 0.8525 (tmm-80) cc_final: 0.8106 (ttt90) REVERT: A 1080 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7616 (tt) REVERT: B 186 MET cc_start: 0.8330 (mpt) cc_final: 0.7897 (mpt) REVERT: B 372 GLU cc_start: 0.8448 (mp0) cc_final: 0.8163 (pm20) REVERT: B 397 LEU cc_start: 0.9255 (tt) cc_final: 0.9011 (pp) REVERT: B 430 MET cc_start: 0.8060 (mmm) cc_final: 0.7444 (tpt) REVERT: B 431 ASP cc_start: 0.8951 (m-30) cc_final: 0.8710 (m-30) REVERT: B 509 MET cc_start: 0.6793 (ttt) cc_final: 0.5819 (mmp) REVERT: B 629 GLU cc_start: 0.8800 (tt0) cc_final: 0.8262 (tt0) REVERT: B 633 SER cc_start: 0.8868 (OUTLIER) cc_final: 0.8652 (p) REVERT: B 656 GLN cc_start: 0.8791 (mt0) cc_final: 0.7904 (mt0) REVERT: B 660 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8255 (mp-120) REVERT: B 804 ASP cc_start: 0.7506 (t0) cc_final: 0.7110 (t0) REVERT: B 827 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7928 (tp30) REVERT: B 828 GLU cc_start: 0.8256 (tp30) cc_final: 0.7986 (tp30) REVERT: B 892 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.8241 (ttt90) REVERT: B 1067 ARG cc_start: 0.8524 (tmm-80) cc_final: 0.8030 (ttt90) REVERT: C 173 HIS cc_start: 0.8831 (t-170) cc_final: 0.8431 (t-170) REVERT: C 186 MET cc_start: 0.8300 (mpt) cc_final: 0.7944 (mpt) REVERT: C 249 PHE cc_start: 0.8182 (t80) cc_final: 0.7937 (t80) REVERT: C 430 MET cc_start: 0.8129 (mmm) cc_final: 0.7531 (tpt) REVERT: C 431 ASP cc_start: 0.9028 (m-30) cc_final: 0.8770 (m-30) REVERT: C 509 MET cc_start: 0.6658 (ttt) cc_final: 0.5732 (mmp) REVERT: C 601 ARG cc_start: 0.8640 (mtp-110) cc_final: 0.8360 (ptm160) REVERT: C 622 MET cc_start: 0.8879 (ttp) cc_final: 0.8414 (ttp) REVERT: C 629 GLU cc_start: 0.8749 (tt0) cc_final: 0.8224 (tt0) REVERT: C 784 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8778 (ttp) REVERT: C 804 ASP cc_start: 0.7545 (t0) cc_final: 0.7265 (t0) REVERT: C 813 LEU cc_start: 0.8724 (mt) cc_final: 0.8487 (mt) REVERT: C 819 PHE cc_start: 0.8926 (t80) cc_final: 0.8487 (t80) REVERT: C 827 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7414 (tp30) REVERT: C 828 GLU cc_start: 0.8322 (tp30) cc_final: 0.8098 (tp30) REVERT: C 857 ARG cc_start: 0.6942 (ttm110) cc_final: 0.6486 (ptp-110) REVERT: C 867 CYS cc_start: 0.7727 (m) cc_final: 0.7466 (t) REVERT: C 892 ARG cc_start: 0.8513 (ttm-80) cc_final: 0.8274 (ttt90) REVERT: C 1067 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8108 (ttt90) REVERT: C 1080 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7682 (tt) REVERT: C 1118 GLU cc_start: 0.8645 (tp30) cc_final: 0.8341 (pp20) REVERT: D 113 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7852 (ttp80) REVERT: D 171 ARG cc_start: 0.7502 (ttm170) cc_final: 0.7044 (ttp80) REVERT: D 186 MET cc_start: 0.8267 (mpt) cc_final: 0.7868 (mpt) REVERT: D 315 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6770 (tm) REVERT: D 509 MET cc_start: 0.6674 (ttt) cc_final: 0.5691 (mmp) REVERT: D 594 LEU cc_start: 0.9558 (tp) cc_final: 0.9311 (tp) REVERT: D 601 ARG cc_start: 0.8510 (mtp-110) cc_final: 0.8252 (ptm160) REVERT: D 622 MET cc_start: 0.8882 (ttp) cc_final: 0.8362 (ttp) REVERT: D 629 GLU cc_start: 0.8744 (tt0) cc_final: 0.8275 (tt0) REVERT: D 633 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8570 (p) REVERT: D 660 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8050 (mp-120) REVERT: D 804 ASP cc_start: 0.7463 (t0) cc_final: 0.7045 (t0) REVERT: D 813 LEU cc_start: 0.8732 (mt) cc_final: 0.8481 (mt) REVERT: D 819 PHE cc_start: 0.8950 (t80) cc_final: 0.8467 (t80) REVERT: D 827 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7645 (tp30) REVERT: D 865 ASN cc_start: 0.8399 (m-40) cc_final: 0.7753 (m110) REVERT: D 882 ARG cc_start: 0.8831 (ttp80) cc_final: 0.8547 (ttp80) REVERT: D 952 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8997 (pt) REVERT: D 1029 LEU cc_start: 0.9557 (tp) cc_final: 0.9152 (tp) REVERT: D 1067 ARG cc_start: 0.8420 (ttp80) cc_final: 0.8085 (ttt90) REVERT: D 1080 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7776 (tt) REVERT: D 1118 GLU cc_start: 0.8651 (tp30) cc_final: 0.8343 (pp20) REVERT: D 1154 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8751 (mtmm) outliers start: 151 outliers final: 95 residues processed: 912 average time/residue: 0.1826 time to fit residues: 266.2430 Evaluate side-chains 862 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 752 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1051 GLN Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 660 GLN Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 874 CYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain C residue 1121 LEU Chi-restraints excluded: chain C residue 1134 LEU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain D residue 1154 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 308 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 165 optimal weight: 0.7980 chunk 268 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 167 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 GLN A 570 ASN A 573 GLN A1108 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN B 573 GLN B 786 ASN B1070 HIS C 570 ASN C 573 GLN C1164 HIS ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN D 866 GLN D1128 HIS D1164 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.177496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.126632 restraints weight = 47130.384| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.75 r_work: 0.3333 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30824 Z= 0.141 Angle : 0.676 9.845 41844 Z= 0.325 Chirality : 0.041 0.275 4716 Planarity : 0.005 0.076 5252 Dihedral : 6.042 59.247 4308 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.05 % Favored : 91.85 % Rotamer: Outliers : 4.70 % Allowed : 22.99 % Favored : 72.31 % 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: -0.72 (0.14), residues: 3728 helix: 0.84 (0.11), residues: 2360 sheet: -3.64 (0.34), residues: 184 loop : -2.68 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 398 TYR 0.024 0.001 TYR A 859 PHE 0.031 0.001 PHE B 454 TRP 0.019 0.002 TRP B 680 HIS 0.014 0.001 HIS B1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (30820) covalent geometry : angle 0.67615 / 0.33 (41836) SS BOND : bond 0.00021 / 0.01 ( 4) SS BOND : angle 0.47198 / 0.24 ( 8) hydrogen bonds : bond 0.03651 / 2.51 ( 1510) hydrogen bonds : angle 4.16581 / 2.87 ( 4470) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 823 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.5381 (mp10) cc_final: 0.5171 (mp10) REVERT: A 173 HIS cc_start: 0.8740 (t70) cc_final: 0.8487 (t-170) REVERT: A 186 MET cc_start: 0.7983 (mpt) cc_final: 0.7569 (mpt) REVERT: A 260 GLN cc_start: 0.7921 (mm110) cc_final: 0.7641 (mm110) REVERT: A 281 ASP cc_start: 0.8031 (m-30) cc_final: 0.7610 (p0) REVERT: A 284 MET cc_start: 0.5700 (tpp) cc_final: 0.5337 (ttp) REVERT: A 454 PHE cc_start: 0.7826 (t80) cc_final: 0.6858 (t80) REVERT: A 459 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.7897 (mtm180) REVERT: A 509 MET cc_start: 0.6842 (ttt) cc_final: 0.6052 (mmp) REVERT: A 629 GLU cc_start: 0.8917 (tt0) cc_final: 0.8550 (tt0) REVERT: A 656 GLN cc_start: 0.8813 (mt0) cc_final: 0.8190 (mt0) REVERT: A 660 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8292 (mp-120) REVERT: A 804 ASP cc_start: 0.7467 (t0) cc_final: 0.7092 (t0) REVERT: A 813 LEU cc_start: 0.8769 (mt) cc_final: 0.8553 (mt) REVERT: A 827 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7969 (tp30) REVERT: A 857 ARG cc_start: 0.6843 (ttm110) cc_final: 0.6422 (ptp-110) REVERT: A 867 CYS cc_start: 0.7957 (m) cc_final: 0.7467 (t) REVERT: A 952 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9042 (pt) REVERT: A 988 MET cc_start: 0.8784 (mtt) cc_final: 0.8459 (mtm) REVERT: A 1029 LEU cc_start: 0.9549 (tp) cc_final: 0.9208 (tp) REVERT: A 1038 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9214 (tp) REVERT: A 1067 ARG cc_start: 0.8473 (tmm-80) cc_final: 0.8034 (ttt90) REVERT: B 171 ARG cc_start: 0.7249 (ttm170) cc_final: 0.7028 (ttp80) REVERT: B 186 MET cc_start: 0.8150 (mpt) cc_final: 0.7774 (mpt) REVERT: B 372 GLU cc_start: 0.8571 (mp0) cc_final: 0.8318 (pm20) REVERT: B 397 LEU cc_start: 0.9234 (tt) cc_final: 0.8975 (pp) REVERT: B 430 MET cc_start: 0.8025 (mmm) cc_final: 0.7448 (tpt) REVERT: B 431 ASP cc_start: 0.8925 (m-30) cc_final: 0.8661 (m-30) REVERT: B 509 MET cc_start: 0.6694 (ttt) cc_final: 0.5727 (mmp) REVERT: B 629 GLU cc_start: 0.8809 (tt0) cc_final: 0.8288 (tt0) REVERT: B 633 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8616 (p) REVERT: B 656 GLN cc_start: 0.8786 (mt0) cc_final: 0.7907 (mt0) REVERT: B 660 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8273 (mp-120) REVERT: B 804 ASP cc_start: 0.7457 (t0) cc_final: 0.7031 (t0) REVERT: B 827 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7869 (tp30) REVERT: B 892 ARG cc_start: 0.8456 (ttm-80) cc_final: 0.8182 (ttt90) REVERT: B 914 LYS cc_start: 0.9178 (ttpm) cc_final: 0.8957 (ttpm) REVERT: B 1067 ARG cc_start: 0.8448 (tmm-80) cc_final: 0.8035 (ttt90) REVERT: C 113 ARG cc_start: 0.8470 (ttt-90) cc_final: 0.8164 (ttt-90) REVERT: C 173 HIS cc_start: 0.8828 (t-170) cc_final: 0.8424 (t-170) REVERT: C 186 MET cc_start: 0.8147 (mpt) cc_final: 0.7928 (mpt) REVERT: C 249 PHE cc_start: 0.8197 (t80) cc_final: 0.7959 (t80) REVERT: C 315 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7332 (tm) REVERT: C 430 MET cc_start: 0.8096 (mmm) cc_final: 0.7420 (tpt) REVERT: C 431 ASP cc_start: 0.9034 (m-30) cc_final: 0.8789 (m-30) REVERT: C 454 PHE cc_start: 0.7051 (t80) cc_final: 0.6445 (t80) REVERT: C 509 MET cc_start: 0.6697 (ttt) cc_final: 0.5781 (mmp) REVERT: C 622 MET cc_start: 0.8865 (ttp) cc_final: 0.8330 (ttp) REVERT: C 629 GLU cc_start: 0.8748 (tt0) cc_final: 0.8245 (tt0) REVERT: C 784 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8792 (ttp) REVERT: C 804 ASP cc_start: 0.7519 (t0) cc_final: 0.7275 (t0) REVERT: C 819 PHE cc_start: 0.8918 (t80) cc_final: 0.8469 (t80) REVERT: C 827 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7365 (tp30) REVERT: C 857 ARG cc_start: 0.6989 (ttm110) cc_final: 0.6536 (ptp-110) REVERT: C 867 CYS cc_start: 0.8093 (m) cc_final: 0.7640 (t) REVERT: C 892 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8242 (ttt90) REVERT: C 1049 LYS cc_start: 0.9182 (mtpp) cc_final: 0.8978 (ttmt) REVERT: C 1064 ARG cc_start: 0.8586 (ttm110) cc_final: 0.8225 (ttp80) REVERT: C 1067 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8083 (ttt90) REVERT: C 1080 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7699 (tt) REVERT: C 1118 GLU cc_start: 0.8595 (tp30) cc_final: 0.8351 (pp20) REVERT: D 113 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7966 (ttp80) REVERT: D 171 ARG cc_start: 0.7538 (ttm170) cc_final: 0.7253 (ttp80) REVERT: D 186 MET cc_start: 0.8116 (mpt) cc_final: 0.7851 (mpt) REVERT: D 315 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6968 (tm) REVERT: D 410 GLN cc_start: 0.9282 (mt0) cc_final: 0.8946 (tp-100) REVERT: D 509 MET cc_start: 0.6713 (ttt) cc_final: 0.5733 (mmp) REVERT: D 594 LEU cc_start: 0.9557 (tp) cc_final: 0.9306 (tp) REVERT: D 601 ARG cc_start: 0.8436 (mtp-110) cc_final: 0.8181 (ptm160) REVERT: D 622 MET cc_start: 0.8893 (ttp) cc_final: 0.8394 (ttp) REVERT: D 629 GLU cc_start: 0.8727 (tt0) cc_final: 0.8313 (tt0) REVERT: D 660 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8069 (mp-120) REVERT: D 804 ASP cc_start: 0.7407 (t0) cc_final: 0.6974 (t0) REVERT: D 813 LEU cc_start: 0.8721 (mt) cc_final: 0.8520 (mt) REVERT: D 827 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7705 (tp30) REVERT: D 882 ARG cc_start: 0.8747 (ttp80) cc_final: 0.8510 (ttp80) REVERT: D 952 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9020 (pt) REVERT: D 1029 LEU cc_start: 0.9559 (tp) cc_final: 0.9147 (tp) REVERT: D 1064 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8317 (ttp-110) REVERT: D 1067 ARG cc_start: 0.8337 (ttp80) cc_final: 0.8060 (ttt90) REVERT: D 1118 GLU cc_start: 0.8635 (tp30) cc_final: 0.8363 (pp20) REVERT: D 1129 LYS cc_start: 0.9114 (ttpt) cc_final: 0.8181 (ptmt) outliers start: 145 outliers final: 102 residues processed: 907 average time/residue: 0.1829 time to fit residues: 267.4467 Evaluate side-chains 869 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 755 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 660 GLN Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain C residue 1134 LEU Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1154 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 353 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 171 optimal weight: 0.6980 chunk 185 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 323 optimal weight: 6.9990 chunk 325 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 ASN A 584 ASN ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN B 573 GLN B1070 HIS C 573 GLN C1128 HIS ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN ** D 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.177668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128082 restraints weight = 47081.912| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.68 r_work: 0.3347 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30824 Z= 0.145 Angle : 0.680 10.578 41844 Z= 0.327 Chirality : 0.041 0.256 4716 Planarity : 0.005 0.066 5252 Dihedral : 5.850 56.565 4308 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.91 % Favored : 91.98 % Rotamer: Outliers : 4.79 % Allowed : 23.51 % Favored : 71.70 % 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: -0.59 (0.14), residues: 3728 helix: 0.94 (0.11), residues: 2360 sheet: -3.60 (0.34), residues: 184 loop : -2.64 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1064 TYR 0.026 0.001 TYR B 859 PHE 0.034 0.002 PHE A 578 TRP 0.021 0.002 TRP C 403 HIS 0.011 0.001 HIS B1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (30820) covalent geometry : angle 0.67972 / 0.33 (41836) SS BOND : bond 0.00021 / 0.01 ( 4) SS BOND : angle 0.48151 / 0.25 ( 8) hydrogen bonds : bond 0.03674 / 2.53 ( 1510) hydrogen bonds : angle 4.17738 / 2.87 ( 4470) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 789 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7976 (mpt) cc_final: 0.7567 (mpt) REVERT: A 260 GLN cc_start: 0.7917 (mm110) cc_final: 0.7659 (mm110) REVERT: A 281 ASP cc_start: 0.7971 (m-30) cc_final: 0.7641 (p0) REVERT: A 430 MET cc_start: 0.8168 (tpt) cc_final: 0.7727 (tpp) REVERT: A 454 PHE cc_start: 0.7756 (t80) cc_final: 0.7513 (t80) REVERT: A 459 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.8097 (mtm-85) REVERT: A 629 GLU cc_start: 0.8906 (tt0) cc_final: 0.8519 (tt0) REVERT: A 660 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8283 (mp-120) REVERT: A 804 ASP cc_start: 0.7443 (t0) cc_final: 0.7019 (t0) REVERT: A 813 LEU cc_start: 0.8770 (mt) cc_final: 0.8566 (mt) REVERT: A 827 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7922 (tp30) REVERT: A 857 ARG cc_start: 0.6842 (ttm110) cc_final: 0.6422 (ptp-110) REVERT: A 867 CYS cc_start: 0.7983 (m) cc_final: 0.7554 (t) REVERT: A 952 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8793 (pt) REVERT: A 988 MET cc_start: 0.8778 (mtt) cc_final: 0.8482 (mtm) REVERT: A 1029 LEU cc_start: 0.9545 (tp) cc_final: 0.9205 (tp) REVERT: A 1038 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9205 (tp) REVERT: A 1067 ARG cc_start: 0.8404 (tmm-80) cc_final: 0.8029 (ttt90) REVERT: B 171 ARG cc_start: 0.7508 (ttm170) cc_final: 0.7199 (ttp80) REVERT: B 186 MET cc_start: 0.8192 (mpt) cc_final: 0.7822 (mpt) REVERT: B 372 GLU cc_start: 0.8577 (mp0) cc_final: 0.8323 (pm20) REVERT: B 397 LEU cc_start: 0.9260 (tt) cc_final: 0.8974 (pp) REVERT: B 430 MET cc_start: 0.8073 (mmm) cc_final: 0.7425 (tpt) REVERT: B 431 ASP cc_start: 0.8896 (m-30) cc_final: 0.8693 (m-30) REVERT: B 509 MET cc_start: 0.6667 (ttt) cc_final: 0.5721 (mmp) REVERT: B 629 GLU cc_start: 0.8807 (tt0) cc_final: 0.8301 (tt0) REVERT: B 633 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8619 (p) REVERT: B 656 GLN cc_start: 0.8770 (mt0) cc_final: 0.8463 (mt0) REVERT: B 804 ASP cc_start: 0.7429 (t0) cc_final: 0.6971 (t0) REVERT: B 827 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7728 (tp30) REVERT: B 892 ARG cc_start: 0.8462 (ttm-80) cc_final: 0.8186 (ttt90) REVERT: B 914 LYS cc_start: 0.9165 (ttpm) cc_final: 0.8949 (ttpm) REVERT: B 1067 ARG cc_start: 0.8414 (tmm-80) cc_final: 0.8055 (ttt90) REVERT: C 113 ARG cc_start: 0.8437 (ttt-90) cc_final: 0.8158 (ttt-90) REVERT: C 173 HIS cc_start: 0.8767 (t-170) cc_final: 0.8502 (t-170) REVERT: C 249 PHE cc_start: 0.8279 (t80) cc_final: 0.7980 (t80) REVERT: C 316 GLU cc_start: 0.7987 (mp0) cc_final: 0.7763 (mp0) REVERT: C 355 MET cc_start: 0.5283 (mmm) cc_final: 0.5027 (mmt) REVERT: C 430 MET cc_start: 0.8182 (mmm) cc_final: 0.7614 (tpt) REVERT: C 431 ASP cc_start: 0.8994 (m-30) cc_final: 0.8790 (m-30) REVERT: C 509 MET cc_start: 0.6734 (ttt) cc_final: 0.5806 (mmp) REVERT: C 629 GLU cc_start: 0.8768 (tt0) cc_final: 0.8318 (tt0) REVERT: C 784 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8777 (ttp) REVERT: C 786 ASN cc_start: 0.8713 (m-40) cc_final: 0.8452 (m-40) REVERT: C 804 ASP cc_start: 0.7482 (t0) cc_final: 0.7205 (t0) REVERT: C 813 LEU cc_start: 0.8705 (mt) cc_final: 0.8491 (mt) REVERT: C 819 PHE cc_start: 0.8958 (t80) cc_final: 0.8482 (t80) REVERT: C 827 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7301 (tp30) REVERT: C 828 GLU cc_start: 0.8215 (tp30) cc_final: 0.7919 (tp30) REVERT: C 857 ARG cc_start: 0.7038 (ttm110) cc_final: 0.6613 (ptp-110) REVERT: C 867 CYS cc_start: 0.7960 (m) cc_final: 0.7562 (t) REVERT: C 892 ARG cc_start: 0.8472 (ttm-80) cc_final: 0.8214 (ttt90) REVERT: C 1067 ARG cc_start: 0.8321 (ttp80) cc_final: 0.8071 (ttt90) REVERT: C 1080 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7684 (tt) REVERT: C 1118 GLU cc_start: 0.8581 (tp30) cc_final: 0.8367 (pp20) REVERT: C 1165 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7967 (pt) REVERT: D 113 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8053 (ttp80) REVERT: D 171 ARG cc_start: 0.7481 (ttm170) cc_final: 0.7150 (ttp80) REVERT: D 186 MET cc_start: 0.8095 (mpt) cc_final: 0.7854 (mpt) REVERT: D 315 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6965 (tm) REVERT: D 430 MET cc_start: 0.8230 (mmm) cc_final: 0.7615 (tpt) REVERT: D 509 MET cc_start: 0.6705 (ttt) cc_final: 0.5767 (mmp) REVERT: D 565 TRP cc_start: 0.8960 (t60) cc_final: 0.8686 (t60) REVERT: D 594 LEU cc_start: 0.9556 (tp) cc_final: 0.9312 (tp) REVERT: D 601 ARG cc_start: 0.8345 (mtp-110) cc_final: 0.8080 (ptm160) REVERT: D 629 GLU cc_start: 0.8737 (tt0) cc_final: 0.8299 (tt0) REVERT: D 660 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8392 (mp10) REVERT: D 804 ASP cc_start: 0.7390 (t0) cc_final: 0.6928 (t0) REVERT: D 827 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7614 (tp30) REVERT: D 882 ARG cc_start: 0.8673 (ttp80) cc_final: 0.8443 (ttp80) REVERT: D 952 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8998 (pt) REVERT: D 1029 LEU cc_start: 0.9558 (tp) cc_final: 0.9149 (tp) REVERT: D 1067 ARG cc_start: 0.8266 (ttp80) cc_final: 0.8045 (ttt90) REVERT: D 1118 GLU cc_start: 0.8620 (tp30) cc_final: 0.8407 (pp20) outliers start: 148 outliers final: 105 residues processed: 875 average time/residue: 0.1815 time to fit residues: 256.1688 Evaluate side-chains 871 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 755 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain D residue 1154 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 278 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 221 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 307 optimal weight: 8.9990 chunk 293 optimal weight: 4.9990 chunk 296 optimal weight: 1.9990 chunk 353 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 573 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN B 573 GLN B 786 ASN B1070 HIS ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 HIS D 573 GLN D 656 GLN ** D 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1128 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.175482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123176 restraints weight = 47275.072| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.54 r_work: 0.3324 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30824 Z= 0.178 Angle : 0.706 13.219 41844 Z= 0.342 Chirality : 0.042 0.248 4716 Planarity : 0.005 0.056 5252 Dihedral : 5.737 59.231 4306 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.15 % Favored : 91.74 % Rotamer: Outliers : 4.92 % Allowed : 23.61 % Favored : 71.47 % 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: -0.57 (0.14), residues: 3728 helix: 0.97 (0.11), residues: 2356 sheet: -3.58 (0.32), residues: 192 loop : -2.63 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 398 TYR 0.029 0.002 TYR B 859 PHE 0.035 0.002 PHE B 578 TRP 0.022 0.002 TRP C 403 HIS 0.019 0.001 HIS B1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (30820) covalent geometry : angle 0.70617 / 0.34 (41836) SS BOND : bond 0.00026 / 0.01 ( 4) SS BOND : angle 0.60555 / 0.32 ( 8) hydrogen bonds : bond 0.03873 / 2.66 ( 1510) hydrogen bonds : angle 4.25504 / 2.92 ( 4470) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 778 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7829 (mpt) cc_final: 0.7435 (mpt) REVERT: A 260 GLN cc_start: 0.8022 (mm110) cc_final: 0.7740 (mm110) REVERT: A 364 TYR cc_start: 0.7276 (t80) cc_final: 0.6645 (t80) REVERT: A 430 MET cc_start: 0.8173 (tpt) cc_final: 0.7694 (tpp) REVERT: A 459 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.8033 (mtm-85) REVERT: A 629 GLU cc_start: 0.8905 (tt0) cc_final: 0.8503 (tt0) REVERT: A 660 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8778 (mp10) REVERT: A 804 ASP cc_start: 0.7482 (t0) cc_final: 0.7037 (t0) REVERT: A 813 LEU cc_start: 0.8767 (mt) cc_final: 0.8548 (mt) REVERT: A 827 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7832 (tp30) REVERT: A 857 ARG cc_start: 0.6868 (ttm110) cc_final: 0.6372 (ptp-110) REVERT: A 867 CYS cc_start: 0.7923 (m) cc_final: 0.7472 (t) REVERT: A 892 ARG cc_start: 0.8600 (ttt90) cc_final: 0.8284 (ttt90) REVERT: A 910 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8884 (m-80) REVERT: A 952 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8971 (pt) REVERT: A 988 MET cc_start: 0.8764 (mtt) cc_final: 0.8460 (mtm) REVERT: A 1038 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9209 (tp) REVERT: A 1067 ARG cc_start: 0.8365 (tmm-80) cc_final: 0.8044 (ttt90) REVERT: B 164 ARG cc_start: 0.7352 (ttt-90) cc_final: 0.7000 (ttt-90) REVERT: B 171 ARG cc_start: 0.7521 (ttm170) cc_final: 0.7200 (ttp80) REVERT: B 186 MET cc_start: 0.8108 (mpt) cc_final: 0.7829 (mpt) REVERT: B 195 ARG cc_start: 0.5343 (OUTLIER) cc_final: 0.4809 (pmt-80) REVERT: B 372 GLU cc_start: 0.8605 (mp0) cc_final: 0.8330 (pm20) REVERT: B 430 MET cc_start: 0.8196 (mmm) cc_final: 0.7503 (tpt) REVERT: B 431 ASP cc_start: 0.8925 (m-30) cc_final: 0.8696 (m-30) REVERT: B 509 MET cc_start: 0.6665 (ttt) cc_final: 0.5725 (mmp) REVERT: B 629 GLU cc_start: 0.8810 (tt0) cc_final: 0.8289 (tt0) REVERT: B 633 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8649 (p) REVERT: B 656 GLN cc_start: 0.8743 (mt0) cc_final: 0.8437 (mt0) REVERT: B 804 ASP cc_start: 0.7459 (t0) cc_final: 0.7000 (t0) REVERT: B 827 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7626 (tp30) REVERT: B 828 GLU cc_start: 0.8261 (tp30) cc_final: 0.8006 (tp30) REVERT: B 892 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8239 (ttt90) REVERT: B 914 LYS cc_start: 0.9179 (ttpm) cc_final: 0.8966 (ttpm) REVERT: B 1067 ARG cc_start: 0.8455 (tmm-80) cc_final: 0.8120 (ttt90) REVERT: C 113 ARG cc_start: 0.8600 (ttt-90) cc_final: 0.8336 (ttt-90) REVERT: C 249 PHE cc_start: 0.8242 (t80) cc_final: 0.7958 (t80) REVERT: C 355 MET cc_start: 0.5477 (mmm) cc_final: 0.5132 (mmt) REVERT: C 412 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8127 (tt0) REVERT: C 430 MET cc_start: 0.8202 (mmm) cc_final: 0.7498 (tpt) REVERT: C 431 ASP cc_start: 0.9032 (m-30) cc_final: 0.8823 (m-30) REVERT: C 433 LEU cc_start: 0.9489 (mt) cc_final: 0.9283 (mt) REVERT: C 509 MET cc_start: 0.6728 (ttt) cc_final: 0.5808 (mmp) REVERT: C 629 GLU cc_start: 0.8765 (tt0) cc_final: 0.8262 (tt0) REVERT: C 784 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8753 (ttp) REVERT: C 804 ASP cc_start: 0.7516 (t0) cc_final: 0.7198 (t0) REVERT: C 813 LEU cc_start: 0.8721 (mt) cc_final: 0.8512 (mt) REVERT: C 827 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7318 (tp30) REVERT: C 857 ARG cc_start: 0.6997 (ttm110) cc_final: 0.6562 (ptp-110) REVERT: C 892 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8238 (ttt90) REVERT: C 941 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8849 (mp) REVERT: C 1067 ARG cc_start: 0.8351 (ttp80) cc_final: 0.8108 (ttt90) REVERT: C 1080 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7642 (tt) REVERT: C 1165 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7986 (pt) REVERT: D 113 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8170 (ttp80) REVERT: D 186 MET cc_start: 0.8007 (mpt) cc_final: 0.7742 (mpt) REVERT: D 315 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7046 (tm) REVERT: D 399 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8449 (pt) REVERT: D 509 MET cc_start: 0.6685 (ttt) cc_final: 0.5745 (mmp) REVERT: D 601 ARG cc_start: 0.8358 (mtp-110) cc_final: 0.8123 (ptm160) REVERT: D 629 GLU cc_start: 0.8697 (tt0) cc_final: 0.8223 (tt0) REVERT: D 660 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8686 (mp10) REVERT: D 804 ASP cc_start: 0.7339 (t0) cc_final: 0.6867 (t0) REVERT: D 827 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7605 (tp30) REVERT: D 857 ARG cc_start: 0.7007 (ttm110) cc_final: 0.6590 (ptp-110) REVERT: D 882 ARG cc_start: 0.8685 (ttp80) cc_final: 0.8456 (ttp80) REVERT: D 952 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8975 (pt) REVERT: D 1067 ARG cc_start: 0.8284 (ttp80) cc_final: 0.8059 (ttt90) outliers start: 152 outliers final: 110 residues processed: 864 average time/residue: 0.1852 time to fit residues: 257.2293 Evaluate side-chains 861 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 736 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 910 PHE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 874 CYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1154 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 183 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 226 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 125 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 304 optimal weight: 9.9990 chunk 295 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 303 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 573 GLN A 656 GLN A 786 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN ** B 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN C 159 HIS ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 HIS C 573 GLN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN D 656 GLN ** D 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.172641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.124323 restraints weight = 47220.689| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.86 r_work: 0.3264 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 30824 Z= 0.225 Angle : 0.752 12.652 41844 Z= 0.366 Chirality : 0.044 0.239 4716 Planarity : 0.005 0.054 5252 Dihedral : 5.801 52.012 4305 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.58 % Favored : 91.31 % Rotamer: Outliers : 4.92 % Allowed : 24.22 % Favored : 70.85 % 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: -0.66 (0.14), residues: 3728 helix: 0.88 (0.11), residues: 2356 sheet: -3.57 (0.32), residues: 192 loop : -2.64 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 332 TYR 0.018 0.002 TYR D1063 PHE 0.042 0.002 PHE A 578 TRP 0.025 0.002 TRP C 403 HIS 0.024 0.001 HIS B1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (30820) covalent geometry : angle 0.75220 / 0.37 (41836) SS BOND : bond 0.00020 / 0.01 ( 4) SS BOND : angle 0.84796 / 0.45 ( 8) hydrogen bonds : bond 0.04132 / 2.86 ( 1510) hydrogen bonds : angle 4.39718 / 3.02 ( 4470) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 769 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7940 (mpt) cc_final: 0.7557 (mpt) REVERT: A 430 MET cc_start: 0.8252 (tpt) cc_final: 0.7740 (tpp) REVERT: A 629 GLU cc_start: 0.8920 (tt0) cc_final: 0.8465 (tt0) REVERT: A 660 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8789 (mp10) REVERT: A 804 ASP cc_start: 0.7539 (t0) cc_final: 0.7085 (t0) REVERT: A 813 LEU cc_start: 0.8782 (mt) cc_final: 0.8530 (mt) REVERT: A 827 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7917 (tp30) REVERT: A 857 ARG cc_start: 0.6888 (ttm110) cc_final: 0.6344 (ptp-110) REVERT: A 876 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9072 (mm) REVERT: A 892 ARG cc_start: 0.8589 (ttt90) cc_final: 0.8297 (ttt90) REVERT: A 910 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.9005 (m-80) REVERT: A 952 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.9006 (pt) REVERT: A 988 MET cc_start: 0.8782 (mtt) cc_final: 0.8474 (mtm) REVERT: A 1038 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9237 (tp) REVERT: A 1067 ARG cc_start: 0.8412 (tmm-80) cc_final: 0.8108 (ttt90) REVERT: B 113 ARG cc_start: 0.8602 (ttt-90) cc_final: 0.8372 (ttt-90) REVERT: B 164 ARG cc_start: 0.7396 (ttt-90) cc_final: 0.7062 (ttt-90) REVERT: B 171 ARG cc_start: 0.7539 (ttm170) cc_final: 0.7234 (ttp80) REVERT: B 186 MET cc_start: 0.8095 (mpt) cc_final: 0.7867 (mpt) REVERT: B 372 GLU cc_start: 0.8636 (mp0) cc_final: 0.8361 (pm20) REVERT: B 430 MET cc_start: 0.8237 (mmm) cc_final: 0.7488 (tpt) REVERT: B 431 ASP cc_start: 0.8961 (m-30) cc_final: 0.8731 (m-30) REVERT: B 509 MET cc_start: 0.6671 (ttt) cc_final: 0.5773 (mmp) REVERT: B 599 MET cc_start: 0.8713 (mtp) cc_final: 0.8284 (ttm) REVERT: B 629 GLU cc_start: 0.8804 (tt0) cc_final: 0.8375 (tt0) REVERT: B 633 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8717 (p) REVERT: B 656 GLN cc_start: 0.8798 (mt0) cc_final: 0.8490 (mt0) REVERT: B 804 ASP cc_start: 0.7548 (t0) cc_final: 0.7097 (t0) REVERT: B 822 PHE cc_start: 0.8885 (t80) cc_final: 0.8677 (t80) REVERT: B 827 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7683 (tp30) REVERT: B 857 ARG cc_start: 0.6844 (ttm110) cc_final: 0.6383 (ptp-110) REVERT: B 892 ARG cc_start: 0.8513 (ttm-80) cc_final: 0.8268 (ttt90) REVERT: B 914 LYS cc_start: 0.9183 (ttpm) cc_final: 0.8979 (ttpm) REVERT: B 1067 ARG cc_start: 0.8485 (tmm-80) cc_final: 0.8196 (ttt90) REVERT: C 113 ARG cc_start: 0.8579 (ttt-90) cc_final: 0.8308 (ttt-90) REVERT: C 249 PHE cc_start: 0.8314 (t80) cc_final: 0.8049 (t80) REVERT: C 355 MET cc_start: 0.5584 (mmm) cc_final: 0.5150 (mmt) REVERT: C 430 MET cc_start: 0.8239 (mmm) cc_final: 0.7526 (tpt) REVERT: C 433 LEU cc_start: 0.9523 (mt) cc_final: 0.9316 (mt) REVERT: C 509 MET cc_start: 0.6773 (ttt) cc_final: 0.5899 (mmp) REVERT: C 629 GLU cc_start: 0.8756 (tt0) cc_final: 0.8356 (tt0) REVERT: C 786 ASN cc_start: 0.8934 (m-40) cc_final: 0.8704 (m-40) REVERT: C 804 ASP cc_start: 0.7598 (t0) cc_final: 0.7283 (t0) REVERT: C 827 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7464 (tp30) REVERT: C 857 ARG cc_start: 0.6942 (ttm110) cc_final: 0.6558 (ptp-110) REVERT: C 941 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9135 (mt) REVERT: C 1067 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8192 (ttt90) REVERT: C 1080 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7542 (tt) REVERT: C 1118 GLU cc_start: 0.8197 (pp20) cc_final: 0.7751 (pp20) REVERT: C 1165 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.8007 (pt) REVERT: D 113 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8133 (ttp80) REVERT: D 173 HIS cc_start: 0.8581 (t-170) cc_final: 0.8258 (t-170) REVERT: D 186 MET cc_start: 0.8014 (mpt) cc_final: 0.7746 (mpt) REVERT: D 315 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6975 (tm) REVERT: D 399 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8474 (pt) REVERT: D 509 MET cc_start: 0.6553 (ttt) cc_final: 0.5703 (mmp) REVERT: D 580 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8919 (mt-10) REVERT: D 601 ARG cc_start: 0.8422 (mtp-110) cc_final: 0.8173 (ptm160) REVERT: D 629 GLU cc_start: 0.8727 (tt0) cc_final: 0.8260 (tt0) REVERT: D 660 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8809 (mp10) REVERT: D 804 ASP cc_start: 0.7469 (t0) cc_final: 0.7002 (t0) REVERT: D 827 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7701 (tp30) REVERT: D 857 ARG cc_start: 0.6948 (ttm110) cc_final: 0.6573 (ptp-110) REVERT: D 952 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9046 (pt) REVERT: D 1067 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8139 (ttt90) outliers start: 152 outliers final: 122 residues processed: 852 average time/residue: 0.1825 time to fit residues: 252.3175 Evaluate side-chains 872 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 736 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 910 PHE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 874 CYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 656 GLN Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 781 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 963 LEU Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1154 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 312 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 287 optimal weight: 6.9990 chunk 210 optimal weight: 8.9990 chunk 373 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 318 optimal weight: 0.9990 chunk 302 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 656 GLN A 786 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN B 573 GLN C 159 HIS ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 GLN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 GLN D 350 GLN ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN ** D 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.176196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128204 restraints weight = 46907.830| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.86 r_work: 0.3322 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30824 Z= 0.150 Angle : 0.721 12.884 41844 Z= 0.349 Chirality : 0.042 0.249 4716 Planarity : 0.005 0.053 5252 Dihedral : 5.654 58.084 4304 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.83 % Favored : 92.06 % Rotamer: Outliers : 3.98 % Allowed : 25.74 % Favored : 70.27 % 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: -0.55 (0.14), residues: 3728 helix: 0.97 (0.11), residues: 2376 sheet: -3.52 (0.33), residues: 192 loop : -2.64 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 334 TYR 0.026 0.001 TYR B 859 PHE 0.045 0.002 PHE B 578 TRP 0.028 0.002 TRP C 403 HIS 0.007 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (30820) covalent geometry : angle 0.72106 / 0.35 (41836) SS BOND : bond 0.00026 / 0.01 ( 4) SS BOND : angle 0.57868 / 0.30 ( 8) hydrogen bonds : bond 0.03830 / 2.64 ( 1510) hydrogen bonds : angle 4.35224 / 2.99 ( 4470) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 805 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7749 (mpt) cc_final: 0.7439 (mpt) REVERT: A 260 GLN cc_start: 0.7891 (mm110) cc_final: 0.7608 (mm110) REVERT: A 430 MET cc_start: 0.8183 (tpt) cc_final: 0.7725 (tpp) REVERT: A 459 ARG cc_start: 0.8298 (mtm-85) cc_final: 0.7830 (mtm-85) REVERT: A 629 GLU cc_start: 0.8949 (tt0) cc_final: 0.8552 (tt0) REVERT: A 776 TRP cc_start: 0.8535 (m100) cc_final: 0.8322 (m100) REVERT: A 804 ASP cc_start: 0.7414 (t0) cc_final: 0.6946 (t0) REVERT: A 813 LEU cc_start: 0.8780 (mt) cc_final: 0.8539 (mt) REVERT: A 827 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7881 (tp30) REVERT: A 857 ARG cc_start: 0.6817 (ttm110) cc_final: 0.6315 (ptp-110) REVERT: A 876 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9033 (mm) REVERT: A 892 ARG cc_start: 0.8490 (ttt90) cc_final: 0.8205 (ttt90) REVERT: A 910 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8918 (m-80) REVERT: A 988 MET cc_start: 0.8798 (mtt) cc_final: 0.8509 (mtm) REVERT: A 1038 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9201 (tp) REVERT: A 1067 ARG cc_start: 0.8328 (tmm-80) cc_final: 0.8010 (ttt90) REVERT: A 1129 LYS cc_start: 0.9147 (ttpp) cc_final: 0.8893 (ttpt) REVERT: B 113 ARG cc_start: 0.8544 (ttt-90) cc_final: 0.8327 (ttt-90) REVERT: B 164 ARG cc_start: 0.7291 (ttt-90) cc_final: 0.6974 (ttt-90) REVERT: B 186 MET cc_start: 0.8102 (mpt) cc_final: 0.7851 (mpt) REVERT: B 289 GLU cc_start: 0.5593 (tp30) cc_final: 0.4948 (tp30) REVERT: B 430 MET cc_start: 0.8225 (mmm) cc_final: 0.7495 (tpt) REVERT: B 431 ASP cc_start: 0.8930 (m-30) cc_final: 0.8729 (m-30) REVERT: B 509 MET cc_start: 0.6659 (ttt) cc_final: 0.5742 (mmp) REVERT: B 629 GLU cc_start: 0.8823 (tt0) cc_final: 0.8301 (tt0) REVERT: B 633 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8636 (p) REVERT: B 786 ASN cc_start: 0.8681 (m-40) cc_final: 0.8425 (m-40) REVERT: B 804 ASP cc_start: 0.7479 (t0) cc_final: 0.6995 (t0) REVERT: B 827 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7653 (tp30) REVERT: B 857 ARG cc_start: 0.6683 (ttm110) cc_final: 0.6255 (ptp-110) REVERT: B 892 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8215 (ttt90) REVERT: B 914 LYS cc_start: 0.9163 (ttpm) cc_final: 0.8960 (ttpm) REVERT: B 1067 ARG cc_start: 0.8383 (tmm-80) cc_final: 0.8077 (ttt90) REVERT: C 113 ARG cc_start: 0.8534 (ttt-90) cc_final: 0.8283 (ttt-90) REVERT: C 249 PHE cc_start: 0.8308 (t80) cc_final: 0.8035 (t80) REVERT: C 262 THR cc_start: 0.7556 (m) cc_final: 0.7206 (p) REVERT: C 412 GLU cc_start: 0.8692 (tp30) cc_final: 0.8303 (tt0) REVERT: C 430 MET cc_start: 0.8203 (mmm) cc_final: 0.7591 (tpt) REVERT: C 509 MET cc_start: 0.6769 (ttt) cc_final: 0.5849 (mmp) REVERT: C 629 GLU cc_start: 0.8764 (tt0) cc_final: 0.8301 (tt0) REVERT: C 804 ASP cc_start: 0.7539 (t0) cc_final: 0.7144 (t0) REVERT: C 827 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7413 (tp30) REVERT: C 857 ARG cc_start: 0.6883 (ttm110) cc_final: 0.6425 (ptp-110) REVERT: C 892 ARG cc_start: 0.8593 (ttt180) cc_final: 0.8265 (ttt90) REVERT: C 1118 GLU cc_start: 0.8277 (pp20) cc_final: 0.7865 (pp20) REVERT: D 113 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8167 (ttp80) REVERT: D 173 HIS cc_start: 0.8603 (t-170) cc_final: 0.8288 (t-170) REVERT: D 186 MET cc_start: 0.7910 (mpt) cc_final: 0.7682 (mpt) REVERT: D 249 PHE cc_start: 0.8178 (t80) cc_final: 0.7842 (t80) REVERT: D 293 GLN cc_start: 0.7195 (mm-40) cc_final: 0.6764 (mm-40) REVERT: D 399 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8391 (pt) REVERT: D 405 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7921 (mtp85) REVERT: D 509 MET cc_start: 0.6789 (ttt) cc_final: 0.5897 (mmp) REVERT: D 576 MET cc_start: 0.8886 (tpp) cc_final: 0.8458 (tpp) REVERT: D 629 GLU cc_start: 0.8724 (tt0) cc_final: 0.8167 (tt0) REVERT: D 660 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8749 (mp10) REVERT: D 804 ASP cc_start: 0.7313 (t0) cc_final: 0.6835 (t0) REVERT: D 827 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7674 (tp30) REVERT: D 857 ARG cc_start: 0.6914 (ttm110) cc_final: 0.6542 (ptp-110) REVERT: D 952 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8806 (pt) outliers start: 123 outliers final: 107 residues processed: 869 average time/residue: 0.1849 time to fit residues: 259.2072 Evaluate side-chains 879 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 764 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 910 PHE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1051 GLN Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 874 CYS Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 164 optimal weight: 0.0970 chunk 301 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 chunk 204 optimal weight: 0.0170 chunk 358 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 281 optimal weight: 0.9990 chunk 298 optimal weight: 0.7980 chunk 114 optimal weight: 0.0870 chunk 16 optimal weight: 0.0020 overall best weight: 0.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 573 GLN A 656 GLN ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN B1070 HIS B1128 HIS C 350 GLN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 ASN C 573 GLN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN D 656 GLN ** D 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.180141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.133838 restraints weight = 47415.139| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.54 r_work: 0.3421 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30824 Z= 0.126 Angle : 0.714 13.041 41844 Z= 0.343 Chirality : 0.041 0.304 4716 Planarity : 0.005 0.054 5252 Dihedral : 5.478 58.691 4304 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.67 % Favored : 92.22 % Rotamer: Outliers : 3.53 % Allowed : 26.65 % Favored : 69.82 % 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: -0.41 (0.14), residues: 3728 helix: 1.06 (0.11), residues: 2368 sheet: -3.45 (0.33), residues: 192 loop : -2.53 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 334 TYR 0.023 0.001 TYR D 364 PHE 0.045 0.001 PHE B 578 TRP 0.033 0.002 TRP C 403 HIS 0.006 0.001 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (30820) covalent geometry : angle 0.71367 / 0.34 (41836) SS BOND : bond 0.00023 / 0.01 ( 4) SS BOND : angle 0.30794 / 0.16 ( 8) hydrogen bonds : bond 0.03621 / 2.47 ( 1510) hydrogen bonds : angle 4.30390 / 2.95 ( 4470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8589.26 seconds wall clock time: 147 minutes 28.09 seconds (8848.09 seconds total)