Starting phenix.real_space_refine on Sat Mar 7 05:42:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nyd_12651/03_2026/7nyd_12651.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nyd_12651/03_2026/7nyd_12651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nyd_12651/03_2026/7nyd_12651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nyd_12651/03_2026/7nyd_12651.map" model { file = "/net/cci-nas-00/data/ceres_data/7nyd_12651/03_2026/7nyd_12651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nyd_12651/03_2026/7nyd_12651.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 256 5.16 5 C 24072 2.51 5 N 6598 2.21 5 O 7500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 226 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38430 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 3914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3914 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 23, 'TRANS': 463} Chain breaks: 2 Chain: "E" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3819 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 468} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3259 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 5977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 5977 Classifications: {'peptide': 809} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 88} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 763} Chain breaks: 2 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 6, 'ASN:plan1': 3, 'TRP:plan': 2, 'GLU:plan': 10, 'TYR:plan': 2, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 167 Chain: "B" Number of atoms: 5631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5631 Classifications: {'peptide': 718} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 680} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2517 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 308} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1319 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain: "A" Number of atoms: 11744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1542, 11744 Classifications: {'peptide': 1542} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1475} Chain breaks: 3 Unresolved non-hydrogen bonds: 495 Unresolved non-hydrogen angles: 632 Unresolved non-hydrogen dihedrals: 413 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLU:plan': 16, 'GLN:plan1': 7, 'ARG:plan': 5, 'ASP:plan': 8, 'TYR:plan': 9, 'ASN:plan1': 5, 'PHE:plan': 7, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 279 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {' CA': 1, 'BMA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {' CA': 1, 'BMA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 26 Unusual residues: {' CA': 1, 'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'BMA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.17, per 1000 atoms: 0.21 Number of scatterers: 38430 At special positions: 0 Unit cell: (236.622, 256.515, 170.661, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 256 16.00 O 7500 8.00 N 6598 7.00 C 24072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=93, symmetry=0 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS D 46 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 56 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 79 " distance=2.03 Simple disulfide: pdb=" SG CYS D 73 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 146 " distance=2.04 Simple disulfide: pdb=" SG CYS D 449 " - pdb=" SG CYS D 496 " distance=2.04 Simple disulfide: pdb=" SG CYS D 451 " - pdb=" SG CYS D 467 " distance=2.05 Simple disulfide: pdb=" SG CYS D 454 " - pdb=" SG CYS D 469 " distance=2.04 Simple disulfide: pdb=" SG CYS D 471 " - pdb=" SG CYS D 480 " distance=2.03 Simple disulfide: pdb=" SG CYS D 503 " - pdb=" SG CYS D 536 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 44 " distance=2.01 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS E 54 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 78 " distance=2.04 Simple disulfide: pdb=" SG CYS E 72 " - pdb=" SG CYS E 91 " distance=2.02 Simple disulfide: pdb=" SG CYS E 85 " - pdb=" SG CYS E 100 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 147 " distance=2.04 Simple disulfide: pdb=" SG CYS E 164 " - pdb=" SG CYS F 40 " distance=2.19 Simple disulfide: pdb=" SG CYS E 467 " - pdb=" SG CYS E 514 " distance=2.02 Simple disulfide: pdb=" SG CYS E 469 " - pdb=" SG CYS E 485 " distance=2.05 Simple disulfide: pdb=" SG CYS E 472 " - pdb=" SG CYS E 487 " distance=2.04 Simple disulfide: pdb=" SG CYS E 489 " - pdb=" SG CYS E 498 " distance=2.02 Simple disulfide: pdb=" SG CYS E 521 " - pdb=" SG CYS E 554 " distance=2.03 Simple disulfide: pdb=" SG CYS E 532 " - pdb=" SG CYS E 544 " distance=2.05 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 57 " distance=2.02 Simple disulfide: pdb=" SG CYS G 33 " - pdb=" SG CYS G 67 " distance=2.03 Simple disulfide: pdb=" SG CYS G 36 " - pdb=" SG CYS G 73 " distance=2.04 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 91 " distance=2.04 Simple disulfide: pdb=" SG CYS G 86 " - pdb=" SG CYS G 104 " distance=2.02 Simple disulfide: pdb=" SG CYS G 98 " - pdb=" SG CYS G 113 " distance=2.04 Simple disulfide: pdb=" SG CYS G 121 " - pdb=" SG CYS G 160 " distance=2.05 Simple disulfide: pdb=" SG CYS G 489 " - pdb=" SG CYS G 505 " distance=2.03 Simple disulfide: pdb=" SG CYS G 492 " - pdb=" SG CYS G 507 " distance=2.03 Simple disulfide: pdb=" SG CYS G 509 " - pdb=" SG CYS G 518 " distance=2.04 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 41 " distance=2.04 Simple disulfide: pdb=" SG CYS C 17 " - pdb=" SG CYS C 51 " distance=2.04 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 57 " distance=1.99 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 87 " distance=2.00 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 97 " distance=2.02 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS C 143 " distance=2.05 Simple disulfide: pdb=" SG CYS C 315 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 411 " - pdb=" SG CYS C 538 " distance=2.04 Simple disulfide: pdb=" SG CYS C 433 " - pdb=" SG CYS C 483 " distance=2.04 Simple disulfide: pdb=" SG CYS C 435 " - pdb=" SG CYS C 451 " distance=2.01 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 453 " distance=2.03 Simple disulfide: pdb=" SG CYS C 455 " - pdb=" SG CYS C 464 " distance=2.05 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 523 " distance=2.05 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 513 " distance=2.04 Simple disulfide: pdb=" SG CYS C 549 " - pdb=" SG CYS C 591 " distance=2.02 Simple disulfide: pdb=" SG CYS C 577 " - pdb=" SG CYS C 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 609 " - pdb=" SG CYS C 651 " distance=2.02 Simple disulfide: pdb=" SG CYS C 637 " - pdb=" SG CYS C 666 " distance=2.02 Simple disulfide: pdb=" SG CYS C 783 " - pdb=" SG CYS C 816 " distance=2.02 Simple disulfide: pdb=" SG CYS B 1 " - pdb=" SG CYS B 40 " distance=2.04 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 44 " distance=2.04 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 57 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 106 " distance=2.01 Simple disulfide: pdb=" SG CYS B 75 " - pdb=" SG CYS B 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 137 " - pdb=" SG CYS B 152 " distance=2.04 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 399 " distance=2.04 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 602 " distance=2.02 Simple disulfide: pdb=" SG CYS B 500 " - pdb=" SG CYS B 549 " distance=2.05 Simple disulfide: pdb=" SG CYS B 502 " - pdb=" SG CYS B 518 " distance=2.02 Simple disulfide: pdb=" SG CYS B 505 " - pdb=" SG CYS B 520 " distance=2.05 Simple disulfide: pdb=" SG CYS B 522 " - pdb=" SG CYS B 531 " distance=2.04 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 580 " distance=2.04 Simple disulfide: pdb=" SG CYS B 623 " - pdb=" SG CYS B 665 " distance=2.04 Simple disulfide: pdb=" SG CYS B 651 " - pdb=" SG CYS B 678 " distance=2.01 Simple disulfide: pdb=" SG CYS B 683 " - pdb=" SG CYS B 725 " distance=2.03 Simple disulfide: pdb=" SG CYS B 711 " - pdb=" SG CYS B 740 " distance=2.03 Simple disulfide: pdb=" SG CYS H 80 " - pdb=" SG CYS H 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 86 " - pdb=" SG CYS H 104 " distance=2.02 Simple disulfide: pdb=" SG CYS H 98 " - pdb=" SG CYS H 113 " distance=2.03 Simple disulfide: pdb=" SG CYS H 121 " - pdb=" SG CYS H 160 " distance=2.03 Simple disulfide: pdb=" SG CYS H 359 " - pdb=" SG CYS H 384 " distance=2.04 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 549 " - pdb=" SG CYS A 792 " distance=2.04 Simple disulfide: pdb=" SG CYS A 616 " - pdb=" SG CYS A 651 " distance=2.02 Simple disulfide: pdb=" SG CYS A 838 " - pdb=" SG CYS A 865 " distance=2.02 Simple disulfide: pdb=" SG CYS A 848 " - pdb=" SG CYS A1509 " distance=2.04 Simple disulfide: pdb=" SG CYS A1083 " - pdb=" SG CYS A1141 " distance=2.03 Simple disulfide: pdb=" SG CYS A1357 " - pdb=" SG CYS A1487 " distance=2.04 Simple disulfide: pdb=" SG CYS A1387 " - pdb=" SG CYS A1456 " distance=2.04 Simple disulfide: pdb=" SG CYS A1502 " - pdb=" SG CYS A1507 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG B1001 " - " ASN B 303 " " NAG G 601 " - " ASN G 394 " " NAG H 601 " - " ASN H 394 " " NAG I 1 " - " ASN D 189 " " NAG J 1 " - " ASN E 407 " " NAG K 1 " - " ASN A 893 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.8 seconds 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9194 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 72 sheets defined 19.8% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.512A pdb=" N LEU D 85 " --> pdb=" O ARG D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.902A pdb=" N TYR D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 386 Processing helix chain 'D' and resid 391 through 403 Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 427 through 447 Processing helix chain 'D' and resid 448 through 451 Processing helix chain 'E' and resid 65 through 69 removed outlier: 3.983A pdb=" N GLN E 68 " --> pdb=" O GLN E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 94 through 98 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 118 through 123 removed outlier: 3.694A pdb=" N ALA E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 290 Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 397 through 407 Processing helix chain 'E' and resid 411 through 421 removed outlier: 3.567A pdb=" N LYS E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 439 removed outlier: 4.315A pdb=" N LEU E 438 " --> pdb=" O ILE E 434 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG E 439 " --> pdb=" O HIS E 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 434 through 439' Processing helix chain 'E' and resid 446 through 464 removed outlier: 3.509A pdb=" N GLN E 459 " --> pdb=" O ARG E 455 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET E 462 " --> pdb=" O ASP E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 469 Processing helix chain 'G' and resid 93 through 97 Processing helix chain 'G' and resid 102 through 106 removed outlier: 4.141A pdb=" N GLY G 105 " --> pdb=" O ASN G 102 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP G 106 " --> pdb=" O ASP G 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 102 through 106' Processing helix chain 'G' and resid 131 through 135 Processing helix chain 'G' and resid 295 through 304 Processing helix chain 'G' and resid 310 through 322 removed outlier: 3.644A pdb=" N PHE G 317 " --> pdb=" O GLU G 313 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR G 320 " --> pdb=" O ALA G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 423 removed outlier: 3.748A pdb=" N GLU G 421 " --> pdb=" O PHE G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 441 Processing helix chain 'G' and resid 456 through 459 Processing helix chain 'G' and resid 465 through 483 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 266 through 278 removed outlier: 3.611A pdb=" N TYR C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 367 Processing helix chain 'C' and resid 377 through 388 Processing helix chain 'C' and resid 403 through 406 Processing helix chain 'C' and resid 411 through 431 removed outlier: 3.678A pdb=" N LEU C 417 " --> pdb=" O SER C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 435 Processing helix chain 'C' and resid 490 through 492 No H-bonds generated for 'chain 'C' and resid 490 through 492' Processing helix chain 'C' and resid 524 through 535 removed outlier: 3.508A pdb=" N LEU C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG C 532 " --> pdb=" O LEU C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 539 Processing helix chain 'C' and resid 720 through 729 Processing helix chain 'C' and resid 771 through 775 removed outlier: 3.546A pdb=" N CYS C 775 " --> pdb=" O ALA C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 804 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.562A pdb=" N ARG B 150 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 314 through 324 Processing helix chain 'B' and resid 329 through 341 removed outlier: 4.031A pdb=" N ILE B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 436 Processing helix chain 'B' and resid 444 through 458 removed outlier: 3.817A pdb=" N GLU B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 473 removed outlier: 3.611A pdb=" N VAL B 473 " --> pdb=" O VAL B 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 470 through 473' Processing helix chain 'B' and resid 478 through 498 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 606 through 610 removed outlier: 3.673A pdb=" N MET B 609 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS B 610 " --> pdb=" O GLU B 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 606 through 610' Processing helix chain 'H' and resid 96 through 100 removed outlier: 4.577A pdb=" N GLY H 100 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 111 removed outlier: 4.218A pdb=" N ASP H 111 " --> pdb=" O SER H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 134 removed outlier: 3.964A pdb=" N THR H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 304 removed outlier: 3.580A pdb=" N ASP H 301 " --> pdb=" O THR H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 321 Processing helix chain 'H' and resid 343 through 348 Processing helix chain 'H' and resid 352 through 361 Processing helix chain 'H' and resid 412 through 425 Processing helix chain 'H' and resid 430 through 441 removed outlier: 3.644A pdb=" N PHE H 434 " --> pdb=" O ASP H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 459 Processing helix chain 'H' and resid 465 through 484 removed outlier: 3.742A pdb=" N ASP H 479 " --> pdb=" O ARG H 475 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE H 481 " --> pdb=" O ILE H 477 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN H 482 " --> pdb=" O GLU H 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 28 Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.695A pdb=" N GLN F 44 " --> pdb=" O CYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 50 Processing helix chain 'F' and resid 93 through 97 removed outlier: 4.109A pdb=" N ALA F 96 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG F 97 " --> pdb=" O LEU F 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 93 through 97' Processing helix chain 'F' and resid 138 through 152 Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 172 through 176 removed outlier: 4.098A pdb=" N VAL F 176 " --> pdb=" O GLN F 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.693A pdb=" N LEU A 74 " --> pdb=" O PRO A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 293 removed outlier: 3.508A pdb=" N ALA A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 590 through 594 Processing helix chain 'A' and resid 604 through 611 Processing helix chain 'A' and resid 623 through 631 Processing helix chain 'A' and resid 642 through 646 Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 991 through 1010 Proline residue: A 999 - end of helix removed outlier: 3.584A pdb=" N TYR A1002 " --> pdb=" O VAL A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1040 removed outlier: 3.547A pdb=" N LYS A1030 " --> pdb=" O LYS A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1073 removed outlier: 4.018A pdb=" N LYS A1073 " --> pdb=" O GLY A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1093 removed outlier: 3.620A pdb=" N ILE A1082 " --> pdb=" O ASN A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1138 Processing helix chain 'A' and resid 1139 through 1141 No H-bonds generated for 'chain 'A' and resid 1139 through 1141' Processing helix chain 'A' and resid 1143 through 1162 removed outlier: 3.880A pdb=" N ASN A1155 " --> pdb=" O ILE A1151 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1179 removed outlier: 3.931A pdb=" N LEU A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1197 removed outlier: 3.563A pdb=" N ARG A1188 " --> pdb=" O HIS A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1244 Processing helix chain 'A' and resid 1245 through 1257 Proline residue: A1251 - end of helix Processing helix chain 'A' and resid 1268 through 1290 removed outlier: 3.517A pdb=" N THR A1272 " --> pdb=" O SER A1268 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A1290 " --> pdb=" O VAL A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1422 Processing helix chain 'A' and resid 1422 through 1427 Processing helix chain 'A' and resid 1526 through 1536 removed outlier: 3.537A pdb=" N ARG A1530 " --> pdb=" O SER A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1557 removed outlier: 4.245A pdb=" N VAL A1557 " --> pdb=" O ASN A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1588 through 1592 removed outlier: 3.788A pdb=" N GLU A1592 " --> pdb=" O THR A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1656 Processing sheet with id=AA1, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'D' and resid 28 through 32 Processing sheet with id=AA3, first strand: chain 'D' and resid 39 through 40 removed outlier: 6.760A pdb=" N SER D 39 " --> pdb=" O CYS D 467 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N CYS D 469 " --> pdb=" O SER D 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'D' and resid 123 through 125 removed outlier: 4.485A pdb=" N GLY D 124 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 148 through 151 Processing sheet with id=AA7, first strand: chain 'D' and resid 162 through 166 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 162 through 166 current: chain 'D' and resid 220 through 252 removed outlier: 6.952A pdb=" N LEU D 296 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N HIS D 249 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA D 294 " --> pdb=" O HIS D 249 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS D 251 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR D 292 " --> pdb=" O LYS D 251 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 351 through 374 current: chain 'E' and resid 133 through 136 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 133 through 136 current: chain 'E' and resid 246 through 273 removed outlier: 5.380A pdb=" N ASN E 247 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N SER E 339 " --> pdb=" O ASN E 247 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU E 249 " --> pdb=" O ILE E 337 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE E 337 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS E 251 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU E 335 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASN E 253 " --> pdb=" O GLU E 333 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLU E 333 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LYS E 255 " --> pdb=" O LYS E 331 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LYS E 331 " --> pdb=" O LYS E 255 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE E 257 " --> pdb=" O LYS E 329 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LYS E 329 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE E 259 " --> pdb=" O ILE E 327 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE E 327 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ARG E 261 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU E 325 " --> pdb=" O ARG E 261 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N PHE E 263 " --> pdb=" O TYR E 323 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR E 323 " --> pdb=" O PHE E 263 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LYS E 265 " --> pdb=" O TYR E 321 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR E 321 " --> pdb=" O LYS E 265 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLN E 267 " --> pdb=" O GLY E 319 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY E 319 " --> pdb=" O GLN E 267 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR E 313 " --> pdb=" O MET E 273 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY E 336 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU E 378 " --> pdb=" O GLY E 336 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR E 338 " --> pdb=" O LYS E 376 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 376 through 394 current: chain 'G' and resid 145 through 147 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 145 through 147 current: chain 'G' and resid 261 through 287 removed outlier: 5.335A pdb=" N LEU G 331 " --> pdb=" O LEU G 282 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG G 284 " --> pdb=" O GLY G 329 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY G 329 " --> pdb=" O ARG G 284 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL G 286 " --> pdb=" O SER G 327 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N SER G 327 " --> pdb=" O VAL G 286 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 393 through 409 current: chain 'C' and resid 129 through 132 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 129 through 132 current: chain 'C' and resid 205 through 241 removed outlier: 6.878A pdb=" N LEU C 287 " --> pdb=" O GLU C 236 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ALA C 238 " --> pdb=" O GLY C 285 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLY C 285 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N PHE C 240 " --> pdb=" O GLN C 283 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLN C 283 " --> pdb=" O PHE C 240 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 330 through 351 current: chain 'B' and resid 182 through 186 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 182 through 186 current: chain 'B' and resid 269 through 306 removed outlier: 7.033A pdb=" N LEU B 350 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN B 303 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY B 348 " --> pdb=" O ASN B 303 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR B 305 " --> pdb=" O THR B 346 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR B 346 " --> pdb=" O THR B 305 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 394 through 424 current: chain 'H' and resid 267 through 272 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 267 through 272 current: chain 'H' and resid 324 through 336 Processing sheet with id=AA8, first strand: chain 'D' and resid 506 through 509 Processing sheet with id=AA9, first strand: chain 'E' and resid 26 through 30 Processing sheet with id=AB1, first strand: chain 'E' and resid 149 through 151 Processing sheet with id=AB2, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AB3, first strand: chain 'E' and resid 477 through 481 Processing sheet with id=AB4, first strand: chain 'E' and resid 527 through 529 Processing sheet with id=AB5, first strand: chain 'G' and resid 20 through 24 removed outlier: 6.422A pdb=" N ASP G 21 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N PHE G 49 " --> pdb=" O ASP G 21 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG G 23 " --> pdb=" O GLU G 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 39 through 43 Processing sheet with id=AB7, first strand: chain 'G' and resid 84 through 85 Processing sheet with id=AB8, first strand: chain 'G' and resid 127 through 128 removed outlier: 6.884A pdb=" N GLU G 127 " --> pdb=" O ARG G 173 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 499 through 501 Processing sheet with id=AC1, first strand: chain 'C' and resid 7 through 8 Processing sheet with id=AC2, first strand: chain 'C' and resid 23 through 27 Processing sheet with id=AC3, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AC4, first strand: chain 'C' and resid 145 through 146 Processing sheet with id=AC5, first strand: chain 'C' and resid 443 through 446 removed outlier: 4.138A pdb=" N LEU C 443 " --> pdb=" O HIS C 454 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 459 through 460 Processing sheet with id=AC7, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AC8, first strand: chain 'C' and resid 558 through 560 Processing sheet with id=AC9, first strand: chain 'C' and resid 581 through 584 Processing sheet with id=AD1, first strand: chain 'C' and resid 608 through 609 Processing sheet with id=AD2, first strand: chain 'C' and resid 619 through 620 removed outlier: 3.605A pdb=" N LEU C 650 " --> pdb=" O SER C 658 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER C 658 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 715 through 719 Processing sheet with id=AD4, first strand: chain 'C' and resid 758 through 760 Processing sheet with id=AD5, first strand: chain 'C' and resid 789 through 794 removed outlier: 6.872A pdb=" N CYS C 783 " --> pdb=" O THR C 811 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 21 through 26 Processing sheet with id=AD7, first strand: chain 'B' and resid 62 through 63 removed outlier: 6.741A pdb=" N LEU B 62 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 78 through 82 Processing sheet with id=AD9, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AE1, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AE2, first strand: chain 'B' and resid 510 through 513 Processing sheet with id=AE3, first strand: chain 'B' and resid 526 through 527 Processing sheet with id=AE4, first strand: chain 'B' and resid 561 through 565 Processing sheet with id=AE5, first strand: chain 'B' and resid 623 through 624 Processing sheet with id=AE6, first strand: chain 'B' and resid 646 through 648 Processing sheet with id=AE7, first strand: chain 'B' and resid 655 through 659 Processing sheet with id=AE8, first strand: chain 'B' and resid 682 through 684 Processing sheet with id=AE9, first strand: chain 'B' and resid 694 through 695 removed outlier: 4.658A pdb=" N GLU B 708 " --> pdb=" O THR B 695 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 84 through 86 removed outlier: 3.728A pdb=" N ARG H 90 " --> pdb=" O CYS H 86 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.581A pdb=" N THR H 170 " --> pdb=" O ASP H 165 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 29 through 37 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 75 through 83 current: chain 'F' and resid 104 through 111 removed outlier: 6.943A pdb=" N VAL F 117 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR F 110 " --> pdb=" O PHE F 115 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE F 115 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 62 through 67 removed outlier: 9.084A pdb=" N ASN A 20 " --> pdb=" O PRO A 10 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 13 through 14 removed outlier: 3.574A pdb=" N SER A 49 " --> pdb=" O ILE A 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 32 through 34 Processing sheet with id=AF7, first strand: chain 'A' and resid 107 through 112 Processing sheet with id=AF8, first strand: chain 'A' and resid 116 through 117 removed outlier: 6.854A pdb=" N THR A 141 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU A 157 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 143 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N MET A 155 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE A 145 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 209 through 215 removed outlier: 3.650A pdb=" N LYS A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 219 through 220 removed outlier: 5.727A pdb=" N LEU A 305 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 335 through 338 removed outlier: 3.775A pdb=" N LYS A 335 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 369 through 377 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 383 through 385 current: chain 'A' and resid 431 through 437 Processing sheet with id=AG4, first strand: chain 'A' and resid 448 through 449 Processing sheet with id=AG5, first strand: chain 'A' and resid 463 through 466 Processing sheet with id=AG6, first strand: chain 'A' and resid 504 through 505 removed outlier: 3.755A pdb=" N SER A 504 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER A 487 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N HIS A 480 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 527 " --> pdb=" O HIS A 480 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 554 through 557 Processing sheet with id=AG8, first strand: chain 'A' and resid 580 through 588 removed outlier: 4.819A pdb=" N ALA A 586 " --> pdb=" O LEU A 756 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU A 756 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASP A 588 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER A 754 " --> pdb=" O ASP A 588 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 754 through 762 current: chain 'A' and resid 790 through 793 Processing sheet with id=AG9, first strand: chain 'A' and resid 805 through 810 removed outlier: 3.916A pdb=" N LYS A 824 " --> pdb=" O ASN A 810 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 815 through 816 removed outlier: 5.793A pdb=" N VAL A 815 " --> pdb=" O VAL A 912 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 835 through 836 Processing sheet with id=AH3, first strand: chain 'A' and resid 916 through 926 removed outlier: 5.552A pdb=" N VAL A 961 " --> pdb=" O ARG A1318 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG A1318 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY A 963 " --> pdb=" O LEU A1316 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU A1316 " --> pdb=" O GLY A 963 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 938 through 941 removed outlier: 6.241A pdb=" N MET A1293 " --> pdb=" O LYS A1309 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS A1309 " --> pdb=" O MET A1293 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE A1295 " --> pdb=" O ASN A1307 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN A1307 " --> pdb=" O ILE A1295 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A1297 " --> pdb=" O LEU A1305 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'A' and resid 1199 through 1201 Processing sheet with id=AH6, first strand: chain 'A' and resid 1359 through 1366 Processing sheet with id=AH7, first strand: chain 'A' and resid 1432 through 1438 removed outlier: 4.104A pdb=" N ASP A1434 " --> pdb=" O GLN A1445 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LYS A1485 " --> pdb=" O GLU A1479 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'A' and resid 1498 through 1499 Processing sheet with id=AH9, first strand: chain 'A' and resid 1560 through 1566 removed outlier: 6.581A pdb=" N LYS A1560 " --> pdb=" O THR A1548 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS A1544 " --> pdb=" O LEU A1564 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ILE A1566 " --> pdb=" O ALA A1542 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ALA A1542 " --> pdb=" O ILE A1566 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A1543 " --> pdb=" O ILE A1601 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3255 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: 9.80 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6959 1.30 - 1.43: 10006 1.43 - 1.56: 21940 1.56 - 1.69: 3 1.69 - 1.82: 322 Bond restraints: 39230 Sorted by residual: bond pdb=" C ASP C 173 " pdb=" O ASP C 173 " ideal model delta sigma weight residual 1.234 1.174 0.061 1.11e-02 8.12e+03 2.97e+01 bond pdb=" CA SER C 15 " pdb=" C SER C 15 " ideal model delta sigma weight residual 1.526 1.452 0.074 1.42e-02 4.96e+03 2.69e+01 bond pdb=" C SER C 15 " pdb=" O SER C 15 " ideal model delta sigma weight residual 1.233 1.171 0.063 1.28e-02 6.10e+03 2.39e+01 bond pdb=" CA TRP C 14 " pdb=" C TRP C 14 " ideal model delta sigma weight residual 1.527 1.466 0.060 1.35e-02 5.49e+03 2.01e+01 bond pdb=" C ILE A 887 " pdb=" O ILE A 887 " ideal model delta sigma weight residual 1.236 1.289 -0.052 1.19e-02 7.06e+03 1.94e+01 ... (remaining 39225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 46139 2.78 - 5.55: 6722 5.55 - 8.33: 268 8.33 - 11.11: 9 11.11 - 13.89: 8 Bond angle restraints: 53146 Sorted by residual: angle pdb=" CA PHE A1209 " pdb=" CB PHE A1209 " pdb=" CG PHE A1209 " ideal model delta sigma weight residual 113.80 125.59 -11.79 1.00e+00 1.00e+00 1.39e+02 angle pdb=" N PRO D 518 " pdb=" CA PRO D 518 " pdb=" C PRO D 518 " ideal model delta sigma weight residual 110.70 121.22 -10.52 1.22e+00 6.72e-01 7.44e+01 angle pdb=" CA ASP E 201 " pdb=" CB ASP E 201 " pdb=" CG ASP E 201 " ideal model delta sigma weight residual 112.60 120.51 -7.91 1.00e+00 1.00e+00 6.26e+01 angle pdb=" CA PHE B 633 " pdb=" CB PHE B 633 " pdb=" CG PHE B 633 " ideal model delta sigma weight residual 113.80 121.55 -7.75 1.00e+00 1.00e+00 6.01e+01 angle pdb=" CA ASN H 465 " pdb=" CB ASN H 465 " pdb=" CG ASN H 465 " ideal model delta sigma weight residual 112.60 119.66 -7.06 1.00e+00 1.00e+00 4.99e+01 ... (remaining 53141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.20: 23129 27.20 - 54.39: 769 54.39 - 81.58: 136 81.58 - 108.78: 52 108.78 - 135.97: 21 Dihedral angle restraints: 24107 sinusoidal: 9788 harmonic: 14319 Sorted by residual: dihedral pdb=" CB CYS A 838 " pdb=" SG CYS A 838 " pdb=" SG CYS A 865 " pdb=" CB CYS A 865 " ideal model delta sinusoidal sigma weight residual -86.00 -171.56 85.56 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CB CYS D 503 " pdb=" SG CYS D 503 " pdb=" SG CYS D 536 " pdb=" CB CYS D 536 " ideal model delta sinusoidal sigma weight residual -86.00 -149.89 63.89 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" C ARG H 348 " pdb=" N ARG H 348 " pdb=" CA ARG H 348 " pdb=" CB ARG H 348 " ideal model delta harmonic sigma weight residual -122.60 -139.08 16.48 0 2.50e+00 1.60e-01 4.35e+01 ... (remaining 24104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.174: 5389 0.174 - 0.348: 443 0.348 - 0.522: 16 0.522 - 0.696: 0 0.696 - 0.870: 3 Chirality restraints: 5851 Sorted by residual: chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.21e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.14e+02 chirality pdb=" C1 MAN K 4 " pdb=" O3 BMA K 3 " pdb=" C2 MAN K 4 " pdb=" O5 MAN K 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.45e+01 ... (remaining 5848 not shown) Planarity restraints: 6950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.356 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG J 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " 0.105 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.545 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1001 " -0.353 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG B1001 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B1001 " -0.073 2.00e-02 2.50e+03 pdb=" N2 NAG B1001 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG B1001 " -0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 601 " 0.332 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG H 601 " -0.096 2.00e-02 2.50e+03 pdb=" C8 NAG H 601 " 0.149 2.00e-02 2.50e+03 pdb=" N2 NAG H 601 " -0.509 2.00e-02 2.50e+03 pdb=" O7 NAG H 601 " 0.124 2.00e-02 2.50e+03 ... (remaining 6947 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 10 2.21 - 2.88: 13378 2.88 - 3.55: 51956 3.55 - 4.23: 88192 4.23 - 4.90: 148063 Nonbonded interactions: 301599 Sorted by model distance: nonbonded pdb=" NH2 ARG D 67 " pdb=" OE2 GLU D 69 " model vdw 1.536 3.120 nonbonded pdb=" CG2 ILE A 887 " pdb=" O VAL A 911 " model vdw 1.908 3.460 nonbonded pdb=" O ASP E 88 " pdb="CA CA E 603 " model vdw 1.972 2.510 nonbonded pdb=" OD1 ASN H 394 " pdb=" C2 NAG H 601 " model vdw 2.044 3.470 nonbonded pdb=" NE2 GLN H 471 " pdb=" O3 BMA G 602 " model vdw 2.079 3.120 ... (remaining 301594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 36.060 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 0.013 0.321 39343 Z= 0.804 Angle : 1.855 27.981 53371 Z= 1.221 Chirality : 0.104 0.870 5851 Planarity : 0.017 0.307 6944 Dihedral : 15.561 135.974 14634 Min Nonbonded Distance : 1.536 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.83 % Favored : 95.15 % Rotamer: Outliers : 0.66 % Allowed : 3.79 % Favored : 95.55 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.04 % 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: -1.14 (0.11), residues: 4890 helix: -1.76 (0.15), residues: 746 sheet: 0.44 (0.14), residues: 1250 loop : -1.03 (0.11), residues: 2894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 90 TYR 0.233 0.023 TYR H 335 PHE 0.108 0.015 PHE H 191 TRP 0.200 0.027 TRP A 542 HIS 0.027 0.004 HIS H 467 Details of bonding type rmsd covalent geometry : bond 0.01258 (39230) covalent geometry : angle 1.84310 (53146) SS BOND : bond 0.01992 ( 93) SS BOND : angle 2.25339 ( 186) hydrogen bonds : bond 0.15929 ( 1212) hydrogen bonds : angle 8.16195 ( 3255) Misc. bond : bond 0.19493 ( 7) link_ALPHA1-2 : bond 0.00129 ( 1) link_ALPHA1-2 : angle 0.91602 ( 3) link_ALPHA1-3 : bond 0.00804 ( 1) link_ALPHA1-3 : angle 2.58827 ( 3) link_BETA1-4 : bond 0.01572 ( 5) link_BETA1-4 : angle 3.39669 ( 15) link_NAG-ASN : bond 0.13953 ( 6) link_NAG-ASN : angle 10.31652 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1302 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 1275 time to evaluate : 1.343 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: 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: D 52 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8715 (mm-30) REVERT: D 71 PHE cc_start: 0.7959 (t80) cc_final: 0.7535 (t80) REVERT: D 116 TRP cc_start: 0.8554 (m-10) cc_final: 0.8287 (m100) REVERT: D 128 PHE cc_start: 0.8882 (m-80) cc_final: 0.8523 (m-80) REVERT: D 141 TYR cc_start: 0.8484 (t80) cc_final: 0.8139 (t80) REVERT: D 155 ARG cc_start: 0.8249 (ptp90) cc_final: 0.7873 (ttm110) REVERT: D 253 LYS cc_start: 0.8554 (mtpt) cc_final: 0.8062 (mtpt) REVERT: D 268 LYS cc_start: 0.8047 (mttt) cc_final: 0.7346 (mtpp) REVERT: D 269 ARG cc_start: 0.8443 (mtt180) cc_final: 0.8130 (ttp-110) REVERT: D 303 THR cc_start: 0.8786 (t) cc_final: 0.8405 (m) REVERT: D 387 GLN cc_start: 0.8605 (pt0) cc_final: 0.7953 (pt0) REVERT: D 405 ASN cc_start: 0.8844 (t0) cc_final: 0.8577 (t0) REVERT: D 432 ARG cc_start: 0.8707 (mtt180) cc_final: 0.7968 (ttm110) REVERT: D 443 GLN cc_start: 0.9067 (tt0) cc_final: 0.8852 (tt0) REVERT: D 446 VAL cc_start: 0.8950 (m) cc_final: 0.7680 (p) REVERT: D 465 SER cc_start: 0.8555 (m) cc_final: 0.8160 (p) REVERT: E 14 TRP cc_start: 0.8437 (m100) cc_final: 0.7214 (m100) REVERT: E 31 ARG cc_start: 0.8348 (mtm180) cc_final: 0.8122 (mtm180) REVERT: E 50 ASP cc_start: 0.8875 (t0) cc_final: 0.8516 (t0) REVERT: E 139 ASP cc_start: 0.9166 (t0) cc_final: 0.8825 (t0) REVERT: E 160 TYR cc_start: 0.8557 (t80) cc_final: 0.8180 (t80) REVERT: E 161 ASP cc_start: 0.8902 (t0) cc_final: 0.8669 (t0) REVERT: E 163 THR cc_start: 0.8322 (p) cc_final: 0.7997 (t) REVERT: E 182 PHE cc_start: 0.8394 (m-80) cc_final: 0.7694 (m-80) REVERT: E 267 GLN cc_start: 0.8724 (mt0) cc_final: 0.8210 (mt0) REVERT: E 275 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8695 (tttp) REVERT: E 277 ASP cc_start: 0.8673 (m-30) cc_final: 0.8435 (t0) REVERT: E 279 MET cc_start: 0.8063 (tpp) cc_final: 0.7797 (tpp) REVERT: E 394 ARG cc_start: 0.8854 (mtt90) cc_final: 0.8402 (ttm110) REVERT: E 408 ARG cc_start: 0.8425 (ttp80) cc_final: 0.7905 (ttp-110) REVERT: E 429 PHE cc_start: 0.7995 (p90) cc_final: 0.7517 (p90) REVERT: E 446 LEU cc_start: 0.8654 (mt) cc_final: 0.8424 (mp) REVERT: E 451 GLN cc_start: 0.8337 (mt0) cc_final: 0.7944 (tp40) REVERT: E 479 ILE cc_start: 0.8210 (mt) cc_final: 0.7429 (tt) REVERT: E 530 ARG cc_start: 0.7346 (mtp180) cc_final: 0.6685 (mtp-110) REVERT: E 531 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7146 (tt0) REVERT: G 40 MET cc_start: 0.7247 (mtm) cc_final: 0.6471 (ttp) REVERT: G 109 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.3002 (m-30) REVERT: G 157 ASN cc_start: 0.8478 (t0) cc_final: 0.7899 (t0) REVERT: G 173 ARG cc_start: 0.8146 (ttp-170) cc_final: 0.7941 (mtp-110) REVERT: G 177 ASN cc_start: 0.8592 (m-40) cc_final: 0.8364 (m-40) REVERT: G 191 PHE cc_start: 0.8517 (t80) cc_final: 0.8132 (t80) REVERT: G 285 PHE cc_start: 0.7679 (p90) cc_final: 0.7375 (p90) REVERT: G 313 GLU cc_start: 0.8253 (tp30) cc_final: 0.7878 (tp30) REVERT: G 461 VAL cc_start: 0.7945 (t) cc_final: 0.6664 (m) REVERT: C 14 TRP cc_start: 0.6499 (m100) cc_final: 0.6139 (m100) REVERT: C 42 VAL cc_start: 0.8250 (m) cc_final: 0.7880 (p) REVERT: C 44 ASN cc_start: 0.8133 (m-40) cc_final: 0.7601 (m-40) REVERT: C 93 ASP cc_start: 0.8599 (p0) cc_final: 0.7668 (p0) REVERT: C 155 TYR cc_start: 0.8736 (m-80) cc_final: 0.8528 (m-80) REVERT: C 295 PHE cc_start: 0.8674 (t80) cc_final: 0.8290 (t80) REVERT: C 304 GLN cc_start: 0.8792 (tt0) cc_final: 0.8282 (tm-30) REVERT: C 495 LYS cc_start: 0.8548 (mttm) cc_final: 0.8250 (mttm) REVERT: C 517 THR cc_start: 0.7925 (m) cc_final: 0.7310 (t) REVERT: C 537 HIS cc_start: 0.9147 (p-80) cc_final: 0.8922 (p-80) REVERT: C 615 MET cc_start: 0.7509 (mtm) cc_final: 0.6854 (mtm) REVERT: C 653 SER cc_start: 0.6332 (OUTLIER) cc_final: 0.6020 (p) REVERT: C 661 MET cc_start: 0.8408 (mpp) cc_final: 0.8181 (mpp) REVERT: B 23 GLN cc_start: 0.8169 (pt0) cc_final: 0.7940 (pt0) REVERT: B 27 ARG cc_start: 0.8418 (mtt90) cc_final: 0.8213 (mtt90) REVERT: B 33 LYS cc_start: 0.7974 (tptt) cc_final: 0.7620 (tptt) REVERT: B 39 PHE cc_start: 0.8303 (m-80) cc_final: 0.8068 (m-80) REVERT: B 76 ILE cc_start: 0.8777 (mm) cc_final: 0.8257 (tp) REVERT: B 101 VAL cc_start: 0.8438 (p) cc_final: 0.7096 (t) REVERT: B 122 LYS cc_start: 0.8851 (mttt) cc_final: 0.8559 (mmtm) REVERT: B 198 LYS cc_start: 0.8535 (ptpt) cc_final: 0.8298 (ptpt) REVERT: B 216 GLU cc_start: 0.8957 (tp30) cc_final: 0.8521 (mm-30) REVERT: B 218 VAL cc_start: 0.8940 (t) cc_final: 0.8262 (p) REVERT: B 226 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8374 (tm-30) REVERT: B 358 TYR cc_start: 0.9110 (t80) cc_final: 0.8743 (t80) REVERT: B 470 VAL cc_start: 0.8740 (p) cc_final: 0.8466 (m) REVERT: B 498 ASP cc_start: 0.8235 (t70) cc_final: 0.6914 (m-30) REVERT: B 566 ARG cc_start: 0.7707 (ptt90) cc_final: 0.7005 (ptt90) REVERT: B 568 CYS cc_start: 0.9054 (m) cc_final: 0.8701 (t) REVERT: B 596 GLU cc_start: 0.8164 (tp30) cc_final: 0.7921 (pm20) REVERT: B 607 GLU cc_start: 0.7769 (pt0) cc_final: 0.7516 (pt0) REVERT: B 630 GLU cc_start: 0.7787 (tt0) cc_final: 0.7400 (pm20) REVERT: B 645 GLU cc_start: 0.7003 (tt0) cc_final: 0.6744 (mm-30) REVERT: B 648 GLU cc_start: 0.8101 (tt0) cc_final: 0.7768 (pm20) REVERT: B 673 GLN cc_start: 0.8650 (tt0) cc_final: 0.8432 (tp40) REVERT: H 93 LYS cc_start: 0.8089 (mptt) cc_final: 0.7765 (mptt) REVERT: H 96 LEU cc_start: 0.7349 (mt) cc_final: 0.6992 (mp) REVERT: H 152 ASP cc_start: 0.8831 (t0) cc_final: 0.8551 (t0) REVERT: H 176 TRP cc_start: 0.8221 (t60) cc_final: 0.7369 (t60) REVERT: H 189 LYS cc_start: 0.8198 (tmtt) cc_final: 0.7566 (mtpt) REVERT: H 192 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7592 (mtp-110) REVERT: H 290 ARG cc_start: 0.8949 (mpt90) cc_final: 0.8466 (mmt-90) REVERT: H 291 ASP cc_start: 0.8590 (t0) cc_final: 0.7623 (t0) REVERT: H 294 LEU cc_start: 0.7156 (mm) cc_final: 0.6927 (mt) REVERT: H 301 ASP cc_start: 0.8442 (t0) cc_final: 0.7681 (t0) REVERT: H 349 LYS cc_start: 0.5991 (mptm) cc_final: 0.5585 (pttt) REVERT: H 357 LYS cc_start: 0.8689 (tttm) cc_final: 0.8432 (tmtt) REVERT: H 448 ILE cc_start: 0.8450 (mt) cc_final: 0.8217 (mp) REVERT: F 27 PHE cc_start: 0.7171 (t80) cc_final: 0.6931 (t80) REVERT: F 51 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7850 (mm-30) REVERT: F 118 LEU cc_start: 0.7499 (mp) cc_final: 0.7288 (mp) REVERT: F 130 LEU cc_start: 0.8702 (tp) cc_final: 0.8501 (tt) REVERT: F 150 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8390 (pt0) REVERT: F 167 PHE cc_start: 0.8755 (m-80) cc_final: 0.8361 (m-80) REVERT: F 173 GLN cc_start: 0.8154 (tt0) cc_final: 0.7949 (tt0) REVERT: A 3 GLN cc_start: 0.8825 (mt0) cc_final: 0.8529 (mp10) REVERT: A 24 GLN cc_start: 0.8864 (tp40) cc_final: 0.8433 (tp40) REVERT: A 104 ASP cc_start: 0.7835 (t0) cc_final: 0.7330 (m-30) REVERT: A 114 LYS cc_start: 0.9176 (mtmt) cc_final: 0.7729 (ttmt) REVERT: A 134 LEU cc_start: 0.7948 (tp) cc_final: 0.7549 (mt) REVERT: A 138 LYS cc_start: 0.8664 (mttt) cc_final: 0.8261 (mtpp) REVERT: A 175 ASN cc_start: 0.8953 (t0) cc_final: 0.8723 (t0) REVERT: A 178 TYR cc_start: 0.8682 (m-80) cc_final: 0.7906 (m-10) REVERT: A 191 PHE cc_start: 0.8863 (m-80) cc_final: 0.8269 (m-80) REVERT: A 193 THR cc_start: 0.8645 (p) cc_final: 0.8140 (m) REVERT: A 196 THR cc_start: 0.9035 (m) cc_final: 0.8747 (t) REVERT: A 223 LYS cc_start: 0.9219 (tttt) cc_final: 0.8975 (mmmt) REVERT: A 225 PHE cc_start: 0.8795 (t80) cc_final: 0.8434 (t80) REVERT: A 242 VAL cc_start: 0.8561 (t) cc_final: 0.8103 (p) REVERT: A 244 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8383 (tm-30) REVERT: A 249 ILE cc_start: 0.8376 (mm) cc_final: 0.8008 (mm) REVERT: A 265 MET cc_start: 0.8714 (mmt) cc_final: 0.8479 (pmm) REVERT: A 304 TYR cc_start: 0.8564 (m-80) cc_final: 0.7781 (m-10) REVERT: A 323 GLU cc_start: 0.8700 (pt0) cc_final: 0.8392 (pt0) REVERT: A 325 PRO cc_start: 0.7986 (Cg_endo) cc_final: 0.7644 (Cg_exo) REVERT: A 357 VAL cc_start: 0.8924 (t) cc_final: 0.8577 (m) REVERT: A 414 GLU cc_start: 0.8362 (pt0) cc_final: 0.8144 (tm-30) REVERT: A 415 PHE cc_start: 0.8696 (p90) cc_final: 0.8395 (p90) REVERT: A 426 GLU cc_start: 0.8485 (tt0) cc_final: 0.8027 (tp30) REVERT: A 475 ILE cc_start: 0.8630 (pt) cc_final: 0.8093 (mt) REVERT: A 541 VAL cc_start: 0.8826 (p) cc_final: 0.8130 (m) REVERT: A 547 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7688 (pp20) REVERT: A 569 THR cc_start: 0.8609 (m) cc_final: 0.8150 (t) REVERT: A 654 ILE cc_start: 0.8474 (pt) cc_final: 0.6868 (tt) REVERT: A 770 PHE cc_start: 0.8824 (p90) cc_final: 0.8545 (p90) REVERT: A 779 TRP cc_start: 0.8869 (m100) cc_final: 0.8024 (m100) REVERT: A 780 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8564 (mt-10) REVERT: A 835 MET cc_start: 0.7375 (ptt) cc_final: 0.7079 (mtt) REVERT: A 880 PHE cc_start: 0.7128 (m-80) cc_final: 0.6781 (m-80) REVERT: A 904 ILE cc_start: 0.6404 (tt) cc_final: 0.5899 (pt) REVERT: A 935 ILE cc_start: 0.8133 (tt) cc_final: 0.7296 (pt) REVERT: A 944 ARG cc_start: 0.8913 (mtt180) cc_final: 0.8642 (mtp-110) REVERT: A 947 LEU cc_start: 0.8157 (mt) cc_final: 0.7881 (pp) REVERT: A 952 LYS cc_start: 0.9010 (ttpt) cc_final: 0.8447 (mmtm) REVERT: A 954 GLU cc_start: 0.8782 (tt0) cc_final: 0.8424 (tm-30) REVERT: A 961 VAL cc_start: 0.8659 (p) cc_final: 0.8120 (t) REVERT: A 981 ILE cc_start: 0.8588 (mt) cc_final: 0.8374 (mt) REVERT: A 1008 GLU cc_start: 0.8542 (tp30) cc_final: 0.8316 (tt0) REVERT: A 1026 LYS cc_start: 0.8836 (tttt) cc_final: 0.8581 (mtpp) REVERT: A 1045 ASP cc_start: 0.7230 (m-30) cc_final: 0.7007 (t70) REVERT: A 1052 LYS cc_start: 0.8397 (mttt) cc_final: 0.8048 (mtmm) REVERT: A 1060 LEU cc_start: 0.8424 (tp) cc_final: 0.7470 (tt) REVERT: A 1096 ASP cc_start: 0.8580 (p0) cc_final: 0.8163 (t70) REVERT: A 1125 TYR cc_start: 0.7622 (t80) cc_final: 0.7255 (t80) REVERT: A 1143 LEU cc_start: 0.8404 (mt) cc_final: 0.8040 (mt) REVERT: A 1197 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8903 (tp30) REVERT: A 1211 LYS cc_start: 0.8805 (mttt) cc_final: 0.8045 (mttm) REVERT: A 1235 TYR cc_start: 0.8238 (m-80) cc_final: 0.7250 (m-10) REVERT: A 1295 ILE cc_start: 0.8429 (mt) cc_final: 0.7566 (tp) REVERT: A 1297 VAL cc_start: 0.8405 (p) cc_final: 0.7626 (t) REVERT: A 1301 HIS cc_start: 0.8426 (m-70) cc_final: 0.8159 (m-70) REVERT: A 1310 MET cc_start: 0.8161 (mmm) cc_final: 0.7941 (mmm) REVERT: A 1316 LEU cc_start: 0.8992 (tp) cc_final: 0.8504 (pt) outliers start: 27 outliers final: 16 residues processed: 1294 average time/residue: 0.2548 time to fit residues: 517.3000 Evaluate side-chains 1093 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 1075 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 413 ARG Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain H residue 348 ARG Chi-restraints excluded: chain H residue 394 ASN Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 887 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 432 optimal weight: 0.4980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 0.5980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 30.0000 chunk 470 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN D 240 HIS D 249 HIS D 260 HIS D 380 HIS D 437 GLN D 443 GLN D 455 GLN E 135 GLN E 488 GLN E 539 ASN G 153 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN C 18 ASN C 73 GLN C 305 ASN B 274 HIS B 625 GLN ** H 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN H 471 GLN F 21 ASN A 54 HIS A 208 HIS A 280 GLN A 301 ASN A 337 ASN A 356 GLN A 482 ASN A 595 GLN A 782 GLN ** A 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 GLN A1103 ASN A1260 GLN A1417 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.173601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.140787 restraints weight = 59996.053| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 3.02 r_work: 0.3702 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 39343 Z= 0.193 Angle : 0.795 15.519 53371 Z= 0.416 Chirality : 0.048 0.431 5851 Planarity : 0.005 0.051 6944 Dihedral : 11.581 111.801 5802 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.47 % Allowed : 11.44 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.11), residues: 4890 helix: -0.39 (0.18), residues: 771 sheet: 0.19 (0.13), residues: 1415 loop : -0.95 (0.11), residues: 2704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 414 TYR 0.020 0.002 TYR E 126 PHE 0.028 0.002 PHE A1187 TRP 0.031 0.003 TRP A 542 HIS 0.008 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00400 (39230) covalent geometry : angle 0.77747 (53146) SS BOND : bond 0.00435 ( 93) SS BOND : angle 2.27808 ( 186) hydrogen bonds : bond 0.04882 ( 1212) hydrogen bonds : angle 6.19732 ( 3255) Misc. bond : bond 0.00286 ( 7) link_ALPHA1-2 : bond 0.00228 ( 1) link_ALPHA1-2 : angle 1.41211 ( 3) link_ALPHA1-3 : bond 0.01569 ( 1) link_ALPHA1-3 : angle 2.98423 ( 3) link_BETA1-4 : bond 0.00753 ( 5) link_BETA1-4 : angle 2.69388 ( 15) link_NAG-ASN : bond 0.00985 ( 6) link_NAG-ASN : angle 5.37968 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 1098 time to evaluate : 1.386 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 TYR cc_start: 0.7495 (m-80) cc_final: 0.7133 (m-80) REVERT: D 32 TYR cc_start: 0.7273 (p90) cc_final: 0.6393 (p90) REVERT: D 52 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6290 (mm-30) REVERT: D 103 ARG cc_start: 0.8054 (mtp180) cc_final: 0.7792 (mtp-110) REVERT: D 127 LEU cc_start: 0.8536 (tp) cc_final: 0.8296 (mp) REVERT: D 140 ARG cc_start: 0.7307 (mtm180) cc_final: 0.6994 (mmm160) REVERT: D 262 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7218 (mm-30) REVERT: D 293 GLU cc_start: 0.6961 (tt0) cc_final: 0.6559 (tt0) REVERT: D 372 LEU cc_start: 0.8358 (tp) cc_final: 0.7915 (tt) REVERT: D 391 THR cc_start: 0.8341 (m) cc_final: 0.7978 (p) REVERT: D 412 LYS cc_start: 0.8066 (mttm) cc_final: 0.7820 (mttm) REVERT: D 441 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7324 (mt-10) REVERT: D 443 GLN cc_start: 0.7515 (tt0) cc_final: 0.7244 (tt0) REVERT: D 465 SER cc_start: 0.8371 (m) cc_final: 0.7886 (p) REVERT: D 475 SER cc_start: 0.8590 (m) cc_final: 0.8228 (p) REVERT: D 481 GLU cc_start: 0.7943 (tt0) cc_final: 0.7706 (tt0) REVERT: D 493 LYS cc_start: 0.7438 (tptt) cc_final: 0.7158 (mptt) REVERT: D 495 ASN cc_start: 0.7924 (p0) cc_final: 0.7699 (p0) REVERT: E 14 TRP cc_start: 0.6835 (m100) cc_final: 0.6307 (m100) REVERT: E 20 CYS cc_start: 0.6873 (m) cc_final: 0.6582 (m) REVERT: E 29 ARG cc_start: 0.7883 (ptt180) cc_final: 0.6592 (ptt180) REVERT: E 121 LYS cc_start: 0.8873 (tptp) cc_final: 0.8653 (tptm) REVERT: E 161 ASP cc_start: 0.7650 (t0) cc_final: 0.7398 (t0) REVERT: E 163 THR cc_start: 0.7283 (p) cc_final: 0.6815 (t) REVERT: E 166 ARG cc_start: 0.7102 (ttt180) cc_final: 0.6771 (ttt180) REVERT: E 181 ASN cc_start: 0.8240 (m-40) cc_final: 0.7988 (m-40) REVERT: E 273 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.6904 (mmm) REVERT: E 275 LYS cc_start: 0.8416 (mmmm) cc_final: 0.8169 (tttp) REVERT: E 454 ARG cc_start: 0.7707 (ttp80) cc_final: 0.7258 (ttp80) REVERT: E 458 ASP cc_start: 0.7604 (m-30) cc_final: 0.7268 (m-30) REVERT: E 462 MET cc_start: 0.7064 (tmm) cc_final: 0.6683 (tmm) REVERT: E 479 ILE cc_start: 0.7672 (mt) cc_final: 0.7338 (tt) REVERT: E 509 ASP cc_start: 0.7838 (p0) cc_final: 0.7438 (p0) REVERT: E 530 ARG cc_start: 0.6982 (mtp180) cc_final: 0.6756 (mtp180) REVERT: E 531 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6610 (tt0) REVERT: E 538 GLN cc_start: 0.8226 (tt0) cc_final: 0.7865 (tt0) REVERT: G 24 MET cc_start: 0.6983 (mtp) cc_final: 0.6749 (mtt) REVERT: G 127 GLU cc_start: 0.7684 (tt0) cc_final: 0.7482 (tt0) REVERT: G 277 LYS cc_start: 0.7375 (ptpp) cc_final: 0.7103 (mtmm) REVERT: G 291 ASP cc_start: 0.7355 (t0) cc_final: 0.7071 (t0) REVERT: G 311 LYS cc_start: 0.7265 (mttm) cc_final: 0.7028 (ttmt) REVERT: G 428 VAL cc_start: 0.7999 (t) cc_final: 0.7688 (m) REVERT: C 107 ASP cc_start: 0.7929 (m-30) cc_final: 0.7698 (m-30) REVERT: C 150 ASP cc_start: 0.7484 (t0) cc_final: 0.7249 (t0) REVERT: C 155 TYR cc_start: 0.8226 (m-80) cc_final: 0.7696 (m-80) REVERT: C 183 TRP cc_start: 0.7481 (t60) cc_final: 0.7154 (t60) REVERT: C 219 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7695 (mt-10) REVERT: C 224 LYS cc_start: 0.8373 (tttt) cc_final: 0.8161 (tttt) REVERT: C 233 ASN cc_start: 0.8029 (t0) cc_final: 0.7829 (t0) REVERT: C 235 VAL cc_start: 0.8579 (m) cc_final: 0.8297 (p) REVERT: C 257 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7382 (tt0) REVERT: C 303 LYS cc_start: 0.7672 (tttt) cc_final: 0.7077 (mtpp) REVERT: C 404 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7625 (mm-30) REVERT: C 407 LYS cc_start: 0.8323 (ttpt) cc_final: 0.8121 (ptmt) REVERT: C 429 GLU cc_start: 0.8158 (tt0) cc_final: 0.7953 (tt0) REVERT: C 436 ARG cc_start: 0.7410 (mtt90) cc_final: 0.7135 (mtm180) REVERT: C 478 ASP cc_start: 0.7243 (m-30) cc_final: 0.6937 (m-30) REVERT: C 487 TRP cc_start: 0.7115 (OUTLIER) cc_final: 0.6473 (m-10) REVERT: C 495 LYS cc_start: 0.7773 (mttm) cc_final: 0.7122 (mttm) REVERT: C 517 THR cc_start: 0.8068 (m) cc_final: 0.7832 (t) REVERT: C 535 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7070 (mm-30) REVERT: C 590 ARG cc_start: 0.7510 (ttm170) cc_final: 0.6990 (ttm170) REVERT: C 606 LYS cc_start: 0.8394 (tttt) cc_final: 0.8192 (ttpp) REVERT: B 23 GLN cc_start: 0.8007 (pt0) cc_final: 0.7637 (pt0) REVERT: B 27 ARG cc_start: 0.8168 (mtt90) cc_final: 0.7869 (mtt90) REVERT: B 39 PHE cc_start: 0.7099 (m-80) cc_final: 0.6867 (m-80) REVERT: B 122 LYS cc_start: 0.8290 (mttt) cc_final: 0.7934 (mmtm) REVERT: B 198 LYS cc_start: 0.8197 (ptpt) cc_final: 0.7860 (ptpt) REVERT: B 216 GLU cc_start: 0.8258 (tp30) cc_final: 0.7657 (tp30) REVERT: B 228 ASP cc_start: 0.7528 (t0) cc_final: 0.7270 (t70) REVERT: B 235 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7765 (mmtm) REVERT: B 243 ASN cc_start: 0.7780 (p0) cc_final: 0.7140 (t0) REVERT: B 297 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8076 (ttmm) REVERT: B 319 LYS cc_start: 0.8340 (tttp) cc_final: 0.8077 (tttp) REVERT: B 358 TYR cc_start: 0.8398 (t80) cc_final: 0.8139 (t80) REVERT: B 359 GLN cc_start: 0.8315 (tt0) cc_final: 0.8079 (tt0) REVERT: B 363 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7253 (tm-30) REVERT: B 437 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6984 (mm-30) REVERT: B 498 ASP cc_start: 0.8120 (t70) cc_final: 0.6706 (m-30) REVERT: B 532 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6781 (tm-30) REVERT: B 533 LYS cc_start: 0.7787 (ptpp) cc_final: 0.7412 (ptpp) REVERT: B 566 ARG cc_start: 0.6477 (ptt90) cc_final: 0.5332 (ptt90) REVERT: B 584 LYS cc_start: 0.8351 (mtpt) cc_final: 0.7895 (mtpt) REVERT: B 606 ASP cc_start: 0.6573 (t70) cc_final: 0.5627 (t0) REVERT: B 639 GLN cc_start: 0.6037 (pm20) cc_final: 0.5669 (pp30) REVERT: B 645 GLU cc_start: 0.6837 (tt0) cc_final: 0.6122 (tt0) REVERT: B 663 PHE cc_start: 0.6960 (m-10) cc_final: 0.6727 (m-10) REVERT: B 723 TYR cc_start: 0.2799 (OUTLIER) cc_final: -0.1197 (m-80) REVERT: B 726 GLN cc_start: 0.6321 (mt0) cc_final: 0.5611 (mp10) REVERT: H 93 LYS cc_start: 0.8194 (mptt) cc_final: 0.7886 (mptt) REVERT: H 127 GLU cc_start: 0.7280 (mt-10) cc_final: 0.7072 (mt-10) REVERT: H 128 GLU cc_start: 0.7456 (pt0) cc_final: 0.7004 (pt0) REVERT: H 152 ASP cc_start: 0.8144 (t0) cc_final: 0.7782 (t0) REVERT: H 189 LYS cc_start: 0.7130 (tmtt) cc_final: 0.6630 (tttm) REVERT: H 195 HIS cc_start: 0.7813 (t70) cc_final: 0.7472 (t-90) REVERT: H 291 ASP cc_start: 0.7634 (t0) cc_final: 0.6805 (t0) REVERT: H 301 ASP cc_start: 0.8078 (t0) cc_final: 0.7870 (t0) REVERT: H 357 LYS cc_start: 0.7756 (tttm) cc_final: 0.7464 (tmtt) REVERT: H 448 ILE cc_start: 0.7469 (mt) cc_final: 0.7142 (mp) REVERT: H 479 ASP cc_start: 0.7860 (t0) cc_final: 0.7611 (t0) REVERT: F 21 ASN cc_start: 0.7916 (t0) cc_final: 0.7613 (t0) REVERT: F 23 ASP cc_start: 0.7988 (t0) cc_final: 0.7346 (p0) REVERT: F 75 ILE cc_start: 0.6752 (OUTLIER) cc_final: 0.5950 (mm) REVERT: F 176 VAL cc_start: 0.8012 (p) cc_final: 0.7727 (m) REVERT: A 24 GLN cc_start: 0.7152 (tp40) cc_final: 0.6456 (tp40) REVERT: A 188 LYS cc_start: 0.7234 (ttmt) cc_final: 0.6958 (ttpp) REVERT: A 216 GLU cc_start: 0.8336 (tp30) cc_final: 0.8111 (tp30) REVERT: A 269 MET cc_start: 0.7440 (pmm) cc_final: 0.7070 (mpp) REVERT: A 270 GLN cc_start: 0.7795 (tt0) cc_final: 0.7479 (mt0) REVERT: A 323 GLU cc_start: 0.7915 (pt0) cc_final: 0.7649 (pt0) REVERT: A 382 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7158 (pt0) REVERT: A 394 ARG cc_start: 0.6698 (mtp85) cc_final: 0.6292 (mtp85) REVERT: A 415 PHE cc_start: 0.8247 (p90) cc_final: 0.8003 (p90) REVERT: A 418 LYS cc_start: 0.8520 (ptpt) cc_final: 0.8149 (ttpp) REVERT: A 432 GLU cc_start: 0.7575 (tp30) cc_final: 0.7346 (tp30) REVERT: A 450 ASP cc_start: 0.7691 (t0) cc_final: 0.7488 (t0) REVERT: A 451 TRP cc_start: 0.8141 (t-100) cc_final: 0.7454 (t60) REVERT: A 482 ASN cc_start: 0.8216 (m110) cc_final: 0.7518 (m-40) REVERT: A 512 VAL cc_start: 0.8025 (OUTLIER) cc_final: 0.7655 (p) REVERT: A 541 VAL cc_start: 0.8824 (p) cc_final: 0.8460 (m) REVERT: A 595 GLN cc_start: 0.8000 (tt0) cc_final: 0.7572 (tm-30) REVERT: A 654 ILE cc_start: 0.7809 (pt) cc_final: 0.7129 (tt) REVERT: A 758 GLU cc_start: 0.7988 (tt0) cc_final: 0.7775 (tt0) REVERT: A 779 TRP cc_start: 0.7971 (m100) cc_final: 0.7399 (m100) REVERT: A 780 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7561 (mt-10) REVERT: A 797 VAL cc_start: 0.8168 (t) cc_final: 0.7846 (m) REVERT: A 800 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7727 (mtmt) REVERT: A 809 MET cc_start: 0.6528 (mmm) cc_final: 0.6165 (mmm) REVERT: A 822 GLN cc_start: 0.7419 (mp10) cc_final: 0.7209 (mm-40) REVERT: A 894 PHE cc_start: 0.6474 (m-80) cc_final: 0.6202 (m-10) REVERT: A 958 ILE cc_start: 0.7731 (mp) cc_final: 0.7521 (tt) REVERT: A 1060 LEU cc_start: 0.8155 (tp) cc_final: 0.7801 (tt) REVERT: A 1143 LEU cc_start: 0.8269 (mt) cc_final: 0.8016 (mt) REVERT: A 1179 LEU cc_start: 0.7934 (mt) cc_final: 0.7725 (mp) REVERT: A 1239 THR cc_start: 0.6747 (m) cc_final: 0.6357 (p) REVERT: A 1248 TYR cc_start: 0.7716 (t80) cc_final: 0.7092 (t80) outliers start: 101 outliers final: 56 residues processed: 1144 average time/residue: 0.2526 time to fit residues: 455.6717 Evaluate side-chains 1064 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 1002 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 514 CYS Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 482 ASN Chi-restraints excluded: chain G residue 513 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 723 TYR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 359 CYS Chi-restraints excluded: chain F residue 64 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 164 LYS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 948 ASP Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 1209 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 134 optimal weight: 8.9990 chunk 312 optimal weight: 9.9990 chunk 347 optimal weight: 0.8980 chunk 322 optimal weight: 0.0980 chunk 223 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 425 optimal weight: 1.9990 chunk 280 optimal weight: 0.7980 chunk 337 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN D 307 ASN E 10 GLN E 432 GLN G 177 ASN G 195 HIS G 275 HIS C 18 ASN C 304 GLN C 347 ASN C 450 HIS B 177 HIS B 367 ASN B 631 ASN B 673 GLN H 465 ASN H 471 GLN F 78 GLN A 52 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN ** A 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1112 GLN A1165 GLN ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1260 GLN A1270 GLN ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.171804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.138994 restraints weight = 60259.331| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 3.06 r_work: 0.3692 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 39343 Z= 0.191 Angle : 0.713 11.589 53371 Z= 0.371 Chirality : 0.047 0.378 5851 Planarity : 0.005 0.053 6944 Dihedral : 9.780 114.334 5772 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.20 % Allowed : 14.01 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.78 (0.11), residues: 4890 helix: -0.17 (0.18), residues: 770 sheet: 0.07 (0.13), residues: 1450 loop : -0.93 (0.11), residues: 2670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 192 TYR 0.025 0.002 TYR E 168 PHE 0.035 0.002 PHE G 285 TRP 0.030 0.002 TRP A 542 HIS 0.010 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00413 (39230) covalent geometry : angle 0.70365 (53146) SS BOND : bond 0.00392 ( 93) SS BOND : angle 1.54948 ( 186) hydrogen bonds : bond 0.04399 ( 1212) hydrogen bonds : angle 5.78824 ( 3255) Misc. bond : bond 0.00084 ( 7) link_ALPHA1-2 : bond 0.00773 ( 1) link_ALPHA1-2 : angle 1.23647 ( 3) link_ALPHA1-3 : bond 0.01083 ( 1) link_ALPHA1-3 : angle 2.39576 ( 3) link_BETA1-4 : bond 0.00691 ( 5) link_BETA1-4 : angle 2.14329 ( 15) link_NAG-ASN : bond 0.00805 ( 6) link_NAG-ASN : angle 4.11867 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 1028 time to evaluate : 1.304 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: D 52 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6332 (mm-30) REVERT: D 120 SER cc_start: 0.7690 (m) cc_final: 0.7404 (t) REVERT: D 127 LEU cc_start: 0.8538 (tp) cc_final: 0.8321 (mp) REVERT: D 140 ARG cc_start: 0.7420 (mtm180) cc_final: 0.7100 (mmm160) REVERT: D 262 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7255 (mm-30) REVERT: D 278 GLU cc_start: 0.7626 (tp30) cc_final: 0.7290 (tp30) REVERT: D 293 GLU cc_start: 0.6927 (tt0) cc_final: 0.6508 (tt0) REVERT: D 306 MET cc_start: 0.7937 (tmm) cc_final: 0.7085 (tmm) REVERT: D 372 LEU cc_start: 0.8397 (tp) cc_final: 0.7911 (tt) REVERT: D 374 ARG cc_start: 0.7919 (mmt180) cc_final: 0.7610 (mpt180) REVERT: D 391 THR cc_start: 0.8403 (m) cc_final: 0.8084 (p) REVERT: D 441 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7276 (mt-10) REVERT: D 443 GLN cc_start: 0.7415 (tt0) cc_final: 0.6991 (mt0) REVERT: D 465 SER cc_start: 0.8429 (m) cc_final: 0.7863 (p) REVERT: D 475 SER cc_start: 0.8651 (m) cc_final: 0.8274 (p) REVERT: D 493 LYS cc_start: 0.7528 (tptt) cc_final: 0.7237 (mptt) REVERT: D 511 GLN cc_start: 0.7310 (mp10) cc_final: 0.6929 (mp10) REVERT: E 14 TRP cc_start: 0.6883 (m100) cc_final: 0.6323 (m100) REVERT: E 20 CYS cc_start: 0.6907 (m) cc_final: 0.6660 (m) REVERT: E 157 GLU cc_start: 0.6814 (tt0) cc_final: 0.6401 (tt0) REVERT: E 161 ASP cc_start: 0.7792 (t0) cc_final: 0.7375 (t0) REVERT: E 163 THR cc_start: 0.7288 (p) cc_final: 0.6697 (t) REVERT: E 166 ARG cc_start: 0.7106 (ttt180) cc_final: 0.6298 (ttp-170) REVERT: E 168 TYR cc_start: 0.7835 (p90) cc_final: 0.7345 (p90) REVERT: E 181 ASN cc_start: 0.8247 (m-40) cc_final: 0.8033 (m-40) REVERT: E 273 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.6737 (mmm) REVERT: E 275 LYS cc_start: 0.8491 (mmmm) cc_final: 0.8276 (tttp) REVERT: E 392 ARG cc_start: 0.7364 (ptp90) cc_final: 0.6931 (ptp-110) REVERT: E 418 ARG cc_start: 0.7308 (ttp-110) cc_final: 0.6808 (mtp85) REVERT: E 423 ASN cc_start: 0.8086 (t0) cc_final: 0.7875 (t0) REVERT: E 454 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7295 (ttp80) REVERT: E 458 ASP cc_start: 0.7663 (m-30) cc_final: 0.7290 (m-30) REVERT: E 462 MET cc_start: 0.7065 (tmm) cc_final: 0.6720 (tmm) REVERT: E 479 ILE cc_start: 0.7622 (mt) cc_final: 0.7310 (tt) REVERT: E 480 LEU cc_start: 0.7478 (mt) cc_final: 0.7256 (tt) REVERT: E 509 ASP cc_start: 0.7907 (p0) cc_final: 0.7545 (p0) REVERT: E 531 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6605 (tt0) REVERT: E 538 GLN cc_start: 0.8218 (tt0) cc_final: 0.7737 (tt0) REVERT: E 539 ASN cc_start: 0.7804 (m-40) cc_final: 0.7406 (m-40) REVERT: G 109 ASP cc_start: 0.6789 (OUTLIER) cc_final: 0.4129 (m-30) REVERT: G 128 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: G 140 ASN cc_start: 0.7920 (t0) cc_final: 0.7690 (t0) REVERT: G 168 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8289 (p) REVERT: G 173 ARG cc_start: 0.7347 (ttt90) cc_final: 0.6814 (ttp-170) REVERT: G 284 ARG cc_start: 0.6758 (ttt90) cc_final: 0.6481 (ttt180) REVERT: G 291 ASP cc_start: 0.7335 (t0) cc_final: 0.7014 (t0) REVERT: G 428 VAL cc_start: 0.8007 (t) cc_final: 0.7685 (m) REVERT: G 479 ASP cc_start: 0.7007 (m-30) cc_final: 0.6671 (m-30) REVERT: C 26 ARG cc_start: 0.7155 (ptt180) cc_final: 0.6898 (ptt90) REVERT: C 66 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7099 (mtp85) REVERT: C 75 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8185 (pt) REVERT: C 142 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7457 (mm-40) REVERT: C 150 ASP cc_start: 0.7519 (t0) cc_final: 0.7312 (t0) REVERT: C 175 ASN cc_start: 0.8189 (t0) cc_final: 0.7851 (m-40) REVERT: C 178 PHE cc_start: 0.8056 (p90) cc_final: 0.7844 (p90) REVERT: C 224 LYS cc_start: 0.8421 (tttt) cc_final: 0.8159 (tttt) REVERT: C 236 GLU cc_start: 0.7176 (mp0) cc_final: 0.6934 (mp0) REVERT: C 303 LYS cc_start: 0.7839 (tttt) cc_final: 0.7210 (mtpp) REVERT: C 355 ILE cc_start: 0.8649 (mt) cc_final: 0.8302 (tt) REVERT: C 404 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7711 (mm-30) REVERT: C 407 LYS cc_start: 0.8325 (ttpt) cc_final: 0.8100 (ptmt) REVERT: C 436 ARG cc_start: 0.7525 (mtt90) cc_final: 0.7238 (mtm180) REVERT: C 478 ASP cc_start: 0.7286 (m-30) cc_final: 0.6868 (m-30) REVERT: C 487 TRP cc_start: 0.7086 (OUTLIER) cc_final: 0.6421 (m-10) REVERT: C 495 LYS cc_start: 0.7888 (mttm) cc_final: 0.7187 (mttm) REVERT: C 535 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7179 (mm-30) REVERT: C 590 ARG cc_start: 0.7596 (ttm170) cc_final: 0.6991 (ttm170) REVERT: C 606 LYS cc_start: 0.8440 (tttt) cc_final: 0.8178 (ttpp) REVERT: C 631 GLU cc_start: 0.6729 (tm-30) cc_final: 0.5971 (tm-30) REVERT: C 632 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7819 (pttt) REVERT: B 23 GLN cc_start: 0.8046 (pt0) cc_final: 0.7628 (pt0) REVERT: B 27 ARG cc_start: 0.8103 (mtt90) cc_final: 0.7846 (mtt90) REVERT: B 37 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7371 (mm-30) REVERT: B 39 PHE cc_start: 0.7186 (m-80) cc_final: 0.6959 (m-80) REVERT: B 198 LYS cc_start: 0.8240 (ptpt) cc_final: 0.7881 (ptpt) REVERT: B 216 GLU cc_start: 0.8247 (tp30) cc_final: 0.7712 (tp30) REVERT: B 226 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6433 (tm-30) REVERT: B 235 LYS cc_start: 0.8082 (mtmm) cc_final: 0.7779 (mmtm) REVERT: B 240 LEU cc_start: 0.7434 (mp) cc_final: 0.7199 (mp) REVERT: B 243 ASN cc_start: 0.7826 (p0) cc_final: 0.7257 (t0) REVERT: B 319 LYS cc_start: 0.8355 (tttp) cc_final: 0.7994 (ttmm) REVERT: B 355 ASP cc_start: 0.8031 (t0) cc_final: 0.7830 (t0) REVERT: B 358 TYR cc_start: 0.8418 (t80) cc_final: 0.8155 (t80) REVERT: B 359 GLN cc_start: 0.8364 (tt0) cc_final: 0.8117 (tt0) REVERT: B 364 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7202 (mp0) REVERT: B 366 LYS cc_start: 0.8180 (mttt) cc_final: 0.7820 (mmtt) REVERT: B 409 GLU cc_start: 0.7513 (tt0) cc_final: 0.7312 (tp30) REVERT: B 437 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7052 (mm-30) REVERT: B 454 SER cc_start: 0.6303 (OUTLIER) cc_final: 0.5578 (p) REVERT: B 498 ASP cc_start: 0.8154 (t70) cc_final: 0.6420 (m-30) REVERT: B 562 ARG cc_start: 0.7746 (ptm160) cc_final: 0.7196 (ptm160) REVERT: B 584 LYS cc_start: 0.8435 (mtpt) cc_final: 0.7948 (mtpt) REVERT: B 606 ASP cc_start: 0.6223 (t0) cc_final: 0.5477 (t0) REVERT: B 610 LYS cc_start: 0.7858 (mtmt) cc_final: 0.7536 (mmmt) REVERT: B 639 GLN cc_start: 0.6135 (pm20) cc_final: 0.5814 (pp30) REVERT: B 663 PHE cc_start: 0.6932 (m-10) cc_final: 0.6702 (m-10) REVERT: B 723 TYR cc_start: 0.3161 (OUTLIER) cc_final: -0.0811 (m-80) REVERT: B 726 GLN cc_start: 0.6623 (mt0) cc_final: 0.5904 (mp10) REVERT: H 93 LYS cc_start: 0.8288 (mptt) cc_final: 0.7887 (mptt) REVERT: H 127 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7129 (mt-10) REVERT: H 128 GLU cc_start: 0.7615 (pt0) cc_final: 0.7075 (pt0) REVERT: H 152 ASP cc_start: 0.8347 (t0) cc_final: 0.8004 (t0) REVERT: H 189 LYS cc_start: 0.7259 (tmtt) cc_final: 0.6879 (tttm) REVERT: H 195 HIS cc_start: 0.7787 (t70) cc_final: 0.7414 (t-90) REVERT: H 279 GLU cc_start: 0.6513 (tm-30) cc_final: 0.6263 (tm-30) REVERT: H 291 ASP cc_start: 0.7239 (t0) cc_final: 0.7001 (t0) REVERT: H 300 ASP cc_start: 0.7522 (m-30) cc_final: 0.7259 (m-30) REVERT: H 305 LEU cc_start: 0.8239 (mt) cc_final: 0.7734 (mt) REVERT: H 319 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7830 (mm-30) REVERT: H 357 LYS cc_start: 0.7719 (tttm) cc_final: 0.7451 (tmtt) REVERT: H 418 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6905 (mt-10) REVERT: H 448 ILE cc_start: 0.7752 (mt) cc_final: 0.7316 (mp) REVERT: H 479 ASP cc_start: 0.7847 (t0) cc_final: 0.7602 (t0) REVERT: F 23 ASP cc_start: 0.8002 (t0) cc_final: 0.7699 (p0) REVERT: F 51 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7042 (mm-30) REVERT: F 112 TYR cc_start: 0.7490 (m-80) cc_final: 0.7140 (m-80) REVERT: F 176 VAL cc_start: 0.7935 (p) cc_final: 0.7686 (m) REVERT: A 4 THR cc_start: 0.8189 (p) cc_final: 0.7974 (t) REVERT: A 24 GLN cc_start: 0.7192 (tp40) cc_final: 0.6409 (tp40) REVERT: A 30 GLU cc_start: 0.7864 (tt0) cc_final: 0.7485 (tm-30) REVERT: A 170 PHE cc_start: 0.7532 (t80) cc_final: 0.7301 (t80) REVERT: A 188 LYS cc_start: 0.7306 (ttmt) cc_final: 0.6976 (ttpp) REVERT: A 216 GLU cc_start: 0.8307 (tp30) cc_final: 0.8072 (tp30) REVERT: A 249 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8333 (tp) REVERT: A 323 GLU cc_start: 0.7903 (pt0) cc_final: 0.7597 (pt0) REVERT: A 371 THR cc_start: 0.8506 (t) cc_final: 0.8298 (t) REVERT: A 382 GLU cc_start: 0.7543 (pt0) cc_final: 0.7223 (pt0) REVERT: A 394 ARG cc_start: 0.6822 (mtp85) cc_final: 0.6375 (mtp85) REVERT: A 415 PHE cc_start: 0.8277 (p90) cc_final: 0.8075 (p90) REVERT: A 418 LYS cc_start: 0.8449 (ptpt) cc_final: 0.8050 (ttpp) REVERT: A 450 ASP cc_start: 0.7787 (t0) cc_final: 0.7443 (t0) REVERT: A 451 TRP cc_start: 0.8124 (t-100) cc_final: 0.7645 (t60) REVERT: A 452 THR cc_start: 0.5412 (OUTLIER) cc_final: 0.4633 (m) REVERT: A 462 GLU cc_start: 0.7734 (pt0) cc_final: 0.7488 (tt0) REVERT: A 482 ASN cc_start: 0.8296 (m110) cc_final: 0.7591 (m110) REVERT: A 524 VAL cc_start: 0.8383 (t) cc_final: 0.8164 (m) REVERT: A 539 ASP cc_start: 0.7957 (t0) cc_final: 0.7641 (t0) REVERT: A 800 LYS cc_start: 0.8301 (mtmt) cc_final: 0.7820 (mttt) REVERT: A 803 LYS cc_start: 0.8016 (pttt) cc_final: 0.7738 (mtmm) REVERT: A 817 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6296 (ttp-170) REVERT: A 822 GLN cc_start: 0.7444 (mp10) cc_final: 0.7181 (mm-40) REVERT: A 839 VAL cc_start: 0.7562 (OUTLIER) cc_final: 0.7156 (m) REVERT: A 840 LYS cc_start: 0.7277 (mmmt) cc_final: 0.6892 (mmmt) REVERT: A 957 ARG cc_start: 0.7468 (mtm180) cc_final: 0.7268 (ptp90) REVERT: A 961 VAL cc_start: 0.8300 (p) cc_final: 0.8080 (t) REVERT: A 993 GLU cc_start: 0.6940 (tt0) cc_final: 0.6565 (pt0) REVERT: A 1026 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8159 (mtpp) REVERT: A 1032 LYS cc_start: 0.8570 (tptt) cc_final: 0.8293 (tptt) REVERT: A 1060 LEU cc_start: 0.8288 (tp) cc_final: 0.7801 (tt) REVERT: A 1090 VAL cc_start: 0.8526 (m) cc_final: 0.8156 (p) REVERT: A 1151 ILE cc_start: 0.8276 (mt) cc_final: 0.7924 (mt) REVERT: A 1197 GLU cc_start: 0.7860 (tp30) cc_final: 0.7334 (tp30) REVERT: A 1273 ILE cc_start: 0.8116 (mt) cc_final: 0.7692 (mp) REVERT: A 1277 GLU cc_start: 0.7569 (tp30) cc_final: 0.7088 (tp30) REVERT: A 1307 ASN cc_start: 0.8078 (p0) cc_final: 0.7674 (p0) outliers start: 131 outliers final: 75 residues processed: 1096 average time/residue: 0.2509 time to fit residues: 438.2685 Evaluate side-chains 1066 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 978 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 429 PHE Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 464 LYS Chi-restraints excluded: chain G residue 482 ASN Chi-restraints excluded: chain G residue 513 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 632 LYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 547 TRP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 683 CYS Chi-restraints excluded: chain B residue 723 TYR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain F residue 64 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 817 ARG Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1344 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 14 optimal weight: 0.7980 chunk 300 optimal weight: 30.0000 chunk 177 optimal weight: 0.9990 chunk 388 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 472 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 346 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 348 optimal weight: 0.9980 chunk 479 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 457 ASN D 495 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 128 GLN B 138 ASN F 78 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 GLN ** A 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 GLN A1184 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.171971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.139244 restraints weight = 60092.832| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.99 r_work: 0.3694 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 39343 Z= 0.182 Angle : 0.685 10.102 53371 Z= 0.356 Chirality : 0.046 0.352 5851 Planarity : 0.005 0.099 6944 Dihedral : 8.811 118.372 5769 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.57 % Allowed : 16.33 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.77 (0.11), residues: 4890 helix: -0.00 (0.18), residues: 771 sheet: 0.01 (0.13), residues: 1482 loop : -0.94 (0.11), residues: 2637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A1228 TYR 0.023 0.002 TYR A 334 PHE 0.025 0.002 PHE C 174 TRP 0.026 0.002 TRP A 542 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00391 (39230) covalent geometry : angle 0.67236 (53146) SS BOND : bond 0.00437 ( 93) SS BOND : angle 1.89393 ( 186) hydrogen bonds : bond 0.04079 ( 1212) hydrogen bonds : angle 5.59663 ( 3255) Misc. bond : bond 0.00053 ( 7) link_ALPHA1-2 : bond 0.00802 ( 1) link_ALPHA1-2 : angle 1.35571 ( 3) link_ALPHA1-3 : bond 0.00970 ( 1) link_ALPHA1-3 : angle 2.43848 ( 3) link_BETA1-4 : bond 0.00410 ( 5) link_BETA1-4 : angle 2.20132 ( 15) link_NAG-ASN : bond 0.00986 ( 6) link_NAG-ASN : angle 3.93952 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 1015 time to evaluate : 1.472 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: D 32 TYR cc_start: 0.7330 (p90) cc_final: 0.6535 (p90) REVERT: D 52 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6374 (mm-30) REVERT: D 102 ARG cc_start: 0.8362 (tpp80) cc_final: 0.8119 (tpp80) REVERT: D 120 SER cc_start: 0.7812 (m) cc_final: 0.7530 (t) REVERT: D 140 ARG cc_start: 0.7448 (mtm180) cc_final: 0.7083 (mmm160) REVERT: D 168 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7780 (mm-40) REVERT: D 262 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7259 (mm-30) REVERT: D 266 ARG cc_start: 0.7424 (ttt90) cc_final: 0.6932 (tpt90) REVERT: D 278 GLU cc_start: 0.7566 (tp30) cc_final: 0.6913 (tp30) REVERT: D 293 GLU cc_start: 0.6892 (tt0) cc_final: 0.6244 (tt0) REVERT: D 301 GLU cc_start: 0.8139 (tt0) cc_final: 0.7829 (tt0) REVERT: D 306 MET cc_start: 0.7970 (tmm) cc_final: 0.7121 (tmm) REVERT: D 372 LEU cc_start: 0.8354 (tp) cc_final: 0.7726 (tt) REVERT: D 374 ARG cc_start: 0.7928 (mmt180) cc_final: 0.7541 (mpt180) REVERT: D 391 THR cc_start: 0.8396 (m) cc_final: 0.8111 (p) REVERT: D 412 LYS cc_start: 0.8092 (mttm) cc_final: 0.7792 (mtmm) REVERT: D 435 MET cc_start: 0.7904 (mtm) cc_final: 0.7690 (mtp) REVERT: D 436 LYS cc_start: 0.7770 (tttm) cc_final: 0.7556 (mtpp) REVERT: D 441 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7141 (mt-10) REVERT: D 443 GLN cc_start: 0.7445 (tt0) cc_final: 0.7002 (mt0) REVERT: D 465 SER cc_start: 0.8308 (m) cc_final: 0.7790 (p) REVERT: D 475 SER cc_start: 0.8652 (m) cc_final: 0.8257 (p) REVERT: D 493 LYS cc_start: 0.7550 (tptt) cc_final: 0.7277 (mptt) REVERT: D 495 ASN cc_start: 0.7969 (OUTLIER) cc_final: 0.7663 (p0) REVERT: D 511 GLN cc_start: 0.7284 (mp10) cc_final: 0.6677 (mp10) REVERT: E 14 TRP cc_start: 0.6907 (m100) cc_final: 0.6399 (m100) REVERT: E 20 CYS cc_start: 0.6916 (m) cc_final: 0.6672 (m) REVERT: E 157 GLU cc_start: 0.6732 (tt0) cc_final: 0.6436 (tt0) REVERT: E 161 ASP cc_start: 0.7790 (t0) cc_final: 0.7362 (t0) REVERT: E 166 ARG cc_start: 0.7105 (ttt180) cc_final: 0.6780 (ttt-90) REVERT: E 178 LYS cc_start: 0.8283 (ttpp) cc_final: 0.7496 (ttpp) REVERT: E 181 ASN cc_start: 0.8266 (m-40) cc_final: 0.7948 (m-40) REVERT: E 273 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.6734 (mmm) REVERT: E 275 LYS cc_start: 0.8490 (mmmm) cc_final: 0.8231 (tttp) REVERT: E 392 ARG cc_start: 0.7351 (ptp90) cc_final: 0.6950 (ptp-110) REVERT: E 423 ASN cc_start: 0.8122 (t0) cc_final: 0.7874 (t0) REVERT: E 462 MET cc_start: 0.7038 (tmm) cc_final: 0.6693 (tmm) REVERT: E 479 ILE cc_start: 0.7633 (mt) cc_final: 0.7319 (tt) REVERT: E 480 LEU cc_start: 0.7537 (mt) cc_final: 0.7207 (tt) REVERT: E 509 ASP cc_start: 0.7922 (p0) cc_final: 0.7605 (p0) REVERT: E 531 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6639 (tt0) REVERT: E 538 GLN cc_start: 0.8182 (tt0) cc_final: 0.7714 (tt0) REVERT: E 539 ASN cc_start: 0.7861 (m-40) cc_final: 0.7420 (m-40) REVERT: G 103 ASP cc_start: 0.7456 (m-30) cc_final: 0.6522 (m-30) REVERT: G 168 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8300 (p) REVERT: G 173 ARG cc_start: 0.7406 (ttt90) cc_final: 0.6949 (ttt-90) REVERT: G 284 ARG cc_start: 0.6702 (ttt90) cc_final: 0.6341 (ttt180) REVERT: G 285 PHE cc_start: 0.7182 (p90) cc_final: 0.6879 (p90) REVERT: G 291 ASP cc_start: 0.7322 (t0) cc_final: 0.7034 (t0) REVERT: G 298 PHE cc_start: 0.8004 (t80) cc_final: 0.7785 (t80) REVERT: G 301 ASP cc_start: 0.7533 (t0) cc_final: 0.7247 (t70) REVERT: G 311 LYS cc_start: 0.7576 (ttmt) cc_final: 0.7339 (ttmt) REVERT: G 409 ARG cc_start: 0.7368 (ptp-170) cc_final: 0.7067 (ptp-170) REVERT: G 428 VAL cc_start: 0.8018 (t) cc_final: 0.7688 (m) REVERT: G 474 GLU cc_start: 0.7572 (tt0) cc_final: 0.7269 (tt0) REVERT: G 479 ASP cc_start: 0.7086 (m-30) cc_final: 0.6876 (m-30) REVERT: C 66 ARG cc_start: 0.7766 (mtp85) cc_final: 0.7051 (mtp85) REVERT: C 75 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8053 (pt) REVERT: C 142 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7317 (mm-40) REVERT: C 175 ASN cc_start: 0.8162 (t0) cc_final: 0.7886 (m-40) REVERT: C 224 LYS cc_start: 0.8413 (tttt) cc_final: 0.8058 (tttt) REVERT: C 236 GLU cc_start: 0.7148 (mp0) cc_final: 0.6854 (mp0) REVERT: C 257 GLU cc_start: 0.7810 (tp30) cc_final: 0.7519 (mm-30) REVERT: C 303 LYS cc_start: 0.7868 (tttt) cc_final: 0.7127 (mtpp) REVERT: C 304 GLN cc_start: 0.7489 (mt0) cc_final: 0.7055 (tm-30) REVERT: C 355 ILE cc_start: 0.8635 (mt) cc_final: 0.8290 (tt) REVERT: C 404 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7717 (mm-30) REVERT: C 426 TYR cc_start: 0.7728 (t80) cc_final: 0.7267 (t80) REVERT: C 436 ARG cc_start: 0.7519 (mtt90) cc_final: 0.7258 (mtm-85) REVERT: C 478 ASP cc_start: 0.7304 (m-30) cc_final: 0.6883 (m-30) REVERT: C 487 TRP cc_start: 0.7043 (OUTLIER) cc_final: 0.6270 (m-10) REVERT: C 495 LYS cc_start: 0.7857 (mttm) cc_final: 0.7195 (mttm) REVERT: C 497 ARG cc_start: 0.6893 (ptt180) cc_final: 0.6658 (ptt180) REVERT: C 517 THR cc_start: 0.8039 (m) cc_final: 0.7675 (t) REVERT: C 535 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7160 (mm-30) REVERT: C 590 ARG cc_start: 0.7584 (ttm170) cc_final: 0.7131 (ttm170) REVERT: C 606 LYS cc_start: 0.8449 (tttt) cc_final: 0.8173 (ttpp) REVERT: C 615 MET cc_start: 0.3713 (mtt) cc_final: 0.2913 (mtt) REVERT: C 632 LYS cc_start: 0.8066 (pttt) cc_final: 0.7857 (pttt) REVERT: C 649 PHE cc_start: 0.6415 (m-10) cc_final: 0.6148 (m-10) REVERT: B 23 GLN cc_start: 0.8093 (pt0) cc_final: 0.7649 (pt0) REVERT: B 27 ARG cc_start: 0.8121 (mtt90) cc_final: 0.7846 (mtt90) REVERT: B 37 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7351 (mm-30) REVERT: B 39 PHE cc_start: 0.7180 (m-80) cc_final: 0.6965 (m-80) REVERT: B 124 ARG cc_start: 0.7771 (ttt-90) cc_final: 0.7477 (ptm-80) REVERT: B 198 LYS cc_start: 0.8258 (ptpt) cc_final: 0.7895 (ptpt) REVERT: B 216 GLU cc_start: 0.8200 (tp30) cc_final: 0.7859 (tp30) REVERT: B 226 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6454 (tm-30) REVERT: B 243 ASN cc_start: 0.7838 (p0) cc_final: 0.7303 (t0) REVERT: B 319 LYS cc_start: 0.8355 (tttp) cc_final: 0.7978 (ttmm) REVERT: B 358 TYR cc_start: 0.8410 (t80) cc_final: 0.7964 (t80) REVERT: B 359 GLN cc_start: 0.8356 (tt0) cc_final: 0.8104 (mt0) REVERT: B 364 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: B 366 LYS cc_start: 0.8180 (mttt) cc_final: 0.7818 (mmtt) REVERT: B 417 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7210 (tt0) REVERT: B 454 SER cc_start: 0.6284 (OUTLIER) cc_final: 0.5525 (p) REVERT: B 498 ASP cc_start: 0.8133 (t70) cc_final: 0.6357 (m-30) REVERT: B 532 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6682 (tm-30) REVERT: B 562 ARG cc_start: 0.7683 (ptm160) cc_final: 0.7103 (ptm160) REVERT: B 566 ARG cc_start: 0.5951 (ptt90) cc_final: 0.5106 (ptt90) REVERT: B 584 LYS cc_start: 0.8396 (mtpt) cc_final: 0.7926 (mtpt) REVERT: B 610 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7565 (mmmt) REVERT: B 639 GLN cc_start: 0.6148 (pm20) cc_final: 0.5893 (pp30) REVERT: B 663 PHE cc_start: 0.6956 (m-10) cc_final: 0.6711 (m-10) REVERT: B 723 TYR cc_start: 0.3095 (OUTLIER) cc_final: -0.0910 (m-80) REVERT: B 726 GLN cc_start: 0.6635 (mt0) cc_final: 0.5926 (mp10) REVERT: H 127 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7106 (mt-10) REVERT: H 128 GLU cc_start: 0.7624 (pt0) cc_final: 0.7106 (pt0) REVERT: H 152 ASP cc_start: 0.8372 (t0) cc_final: 0.8038 (t0) REVERT: H 164 ARG cc_start: 0.5193 (OUTLIER) cc_final: 0.4898 (ptt90) REVERT: H 195 HIS cc_start: 0.7762 (t70) cc_final: 0.7474 (t-90) REVERT: H 279 GLU cc_start: 0.6336 (tm-30) cc_final: 0.5655 (tm-30) REVERT: H 291 ASP cc_start: 0.7369 (t0) cc_final: 0.7051 (t0) REVERT: H 409 ARG cc_start: 0.7082 (mtp180) cc_final: 0.6775 (mtp-110) REVERT: H 418 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6838 (mt-10) REVERT: H 448 ILE cc_start: 0.7844 (mt) cc_final: 0.7439 (mp) REVERT: H 479 ASP cc_start: 0.7901 (t70) cc_final: 0.7659 (t70) REVERT: H 484 PHE cc_start: 0.6498 (m-80) cc_final: 0.5894 (m-80) REVERT: F 51 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7038 (mm-30) REVERT: F 158 GLN cc_start: 0.8213 (mt0) cc_final: 0.7688 (tt0) REVERT: F 176 VAL cc_start: 0.7871 (p) cc_final: 0.7600 (m) REVERT: A 4 THR cc_start: 0.8201 (p) cc_final: 0.8000 (t) REVERT: A 24 GLN cc_start: 0.7182 (tp40) cc_final: 0.6723 (tp40) REVERT: A 30 GLU cc_start: 0.7851 (tt0) cc_final: 0.7400 (tm-30) REVERT: A 170 PHE cc_start: 0.7472 (t80) cc_final: 0.6995 (t80) REVERT: A 188 LYS cc_start: 0.7211 (ttmt) cc_final: 0.6834 (ttpp) REVERT: A 216 GLU cc_start: 0.8283 (tp30) cc_final: 0.8063 (tp30) REVERT: A 249 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8339 (tp) REVERT: A 323 GLU cc_start: 0.7880 (pt0) cc_final: 0.7606 (pt0) REVERT: A 371 THR cc_start: 0.8509 (t) cc_final: 0.8289 (t) REVERT: A 382 GLU cc_start: 0.7475 (pt0) cc_final: 0.7176 (pt0) REVERT: A 394 ARG cc_start: 0.6879 (mtp85) cc_final: 0.6424 (mtp85) REVERT: A 415 PHE cc_start: 0.8295 (p90) cc_final: 0.8047 (p90) REVERT: A 418 LYS cc_start: 0.8359 (ptpt) cc_final: 0.8085 (ttpp) REVERT: A 450 ASP cc_start: 0.7878 (t0) cc_final: 0.7504 (t0) REVERT: A 451 TRP cc_start: 0.8086 (t-100) cc_final: 0.7696 (t60) REVERT: A 462 GLU cc_start: 0.7754 (pt0) cc_final: 0.7403 (pt0) REVERT: A 524 VAL cc_start: 0.8402 (t) cc_final: 0.8165 (m) REVERT: A 539 ASP cc_start: 0.8023 (t0) cc_final: 0.7618 (t0) REVERT: A 541 VAL cc_start: 0.8850 (p) cc_final: 0.8465 (m) REVERT: A 755 TRP cc_start: 0.8295 (p-90) cc_final: 0.7792 (p-90) REVERT: A 784 VAL cc_start: 0.8607 (t) cc_final: 0.8253 (m) REVERT: A 800 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7889 (mttt) REVERT: A 803 LYS cc_start: 0.7848 (pttt) cc_final: 0.7638 (mtmm) REVERT: A 822 GLN cc_start: 0.7617 (mp10) cc_final: 0.7307 (mm-40) REVERT: A 839 VAL cc_start: 0.7689 (OUTLIER) cc_final: 0.7262 (m) REVERT: A 840 LYS cc_start: 0.7369 (mmmt) cc_final: 0.7030 (mmmt) REVERT: A 892 ILE cc_start: 0.7803 (mt) cc_final: 0.7575 (mm) REVERT: A 961 VAL cc_start: 0.8247 (p) cc_final: 0.7924 (t) REVERT: A 962 LYS cc_start: 0.7314 (mmmm) cc_final: 0.7023 (mmmm) REVERT: A 975 SER cc_start: 0.7959 (t) cc_final: 0.7633 (t) REVERT: A 993 GLU cc_start: 0.6881 (tt0) cc_final: 0.6596 (pt0) REVERT: A 1008 GLU cc_start: 0.7627 (tp30) cc_final: 0.7402 (mt-10) REVERT: A 1026 LYS cc_start: 0.8506 (ttmt) cc_final: 0.8176 (mtpp) REVERT: A 1060 LEU cc_start: 0.8280 (tp) cc_final: 0.7732 (tt) REVERT: A 1076 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6715 (tm-30) REVERT: A 1079 GLN cc_start: 0.8425 (mp10) cc_final: 0.7993 (mp10) REVERT: A 1151 ILE cc_start: 0.8299 (mt) cc_final: 0.7945 (mt) REVERT: A 1197 GLU cc_start: 0.7818 (tp30) cc_final: 0.7274 (tp30) REVERT: A 1228 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7372 (tpt90) REVERT: A 1273 ILE cc_start: 0.8133 (mt) cc_final: 0.7929 (mm) REVERT: A 1277 GLU cc_start: 0.7486 (tp30) cc_final: 0.6964 (tp30) REVERT: A 1307 ASN cc_start: 0.8068 (p0) cc_final: 0.7788 (p0) outliers start: 146 outliers final: 89 residues processed: 1082 average time/residue: 0.2601 time to fit residues: 444.9868 Evaluate side-chains 1072 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 970 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 666 CYS Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 547 TRP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 683 CYS Chi-restraints excluded: chain B residue 723 TYR Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain F residue 64 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1344 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 261 optimal weight: 0.0970 chunk 462 optimal weight: 0.0020 chunk 37 optimal weight: 1.9990 chunk 484 optimal weight: 10.0000 chunk 367 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 341 optimal weight: 0.6980 chunk 364 optimal weight: 6.9990 chunk 389 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 457 ASN E 435 HIS E 459 GLN G 161 ASN G 281 HIS G 289 ASN G 472 ASN C 18 ASN C 128 GLN B 367 ASN H 457 ASN F 78 GLN A 3 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN A 782 GLN ** A 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1184 HIS A1274 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.173251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.140723 restraints weight = 60078.871| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 3.01 r_work: 0.3715 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 39343 Z= 0.136 Angle : 0.645 10.558 53371 Z= 0.332 Chirality : 0.044 0.328 5851 Planarity : 0.005 0.097 6944 Dihedral : 7.983 116.524 5768 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.45 % Allowed : 17.55 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.12), residues: 4890 helix: 0.28 (0.19), residues: 759 sheet: 0.06 (0.13), residues: 1451 loop : -0.81 (0.12), residues: 2680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1228 TYR 0.015 0.002 TYR E 321 PHE 0.021 0.001 PHE C 147 TRP 0.020 0.002 TRP E 416 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00298 (39230) covalent geometry : angle 0.63556 (53146) SS BOND : bond 0.00270 ( 93) SS BOND : angle 1.57840 ( 186) hydrogen bonds : bond 0.03707 ( 1212) hydrogen bonds : angle 5.38542 ( 3255) Misc. bond : bond 0.00076 ( 7) link_ALPHA1-2 : bond 0.00729 ( 1) link_ALPHA1-2 : angle 1.32756 ( 3) link_ALPHA1-3 : bond 0.00836 ( 1) link_ALPHA1-3 : angle 2.26308 ( 3) link_BETA1-4 : bond 0.00411 ( 5) link_BETA1-4 : angle 1.96195 ( 15) link_NAG-ASN : bond 0.00679 ( 6) link_NAG-ASN : angle 3.20686 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1009 time to evaluate : 1.506 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: D 32 TYR cc_start: 0.7227 (p90) cc_final: 0.6445 (p90) REVERT: D 52 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6331 (mm-30) REVERT: D 97 ASP cc_start: 0.6634 (p0) cc_final: 0.6268 (p0) REVERT: D 102 ARG cc_start: 0.8312 (tpp80) cc_final: 0.8077 (tpp80) REVERT: D 120 SER cc_start: 0.7797 (m) cc_final: 0.7538 (t) REVERT: D 128 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7753 (m-80) REVERT: D 140 ARG cc_start: 0.7432 (mtm180) cc_final: 0.7134 (mmm160) REVERT: D 187 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6908 (mt-10) REVERT: D 253 LYS cc_start: 0.7567 (mtmt) cc_final: 0.7128 (mtpt) REVERT: D 284 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7987 (mtm-85) REVERT: D 293 GLU cc_start: 0.6914 (tt0) cc_final: 0.6518 (tt0) REVERT: D 306 MET cc_start: 0.7924 (tmm) cc_final: 0.7443 (tmm) REVERT: D 372 LEU cc_start: 0.8337 (tp) cc_final: 0.7716 (tt) REVERT: D 374 ARG cc_start: 0.7928 (mmt180) cc_final: 0.7609 (mpt180) REVERT: D 391 THR cc_start: 0.8304 (m) cc_final: 0.8006 (p) REVERT: D 429 SER cc_start: 0.8529 (m) cc_final: 0.8117 (t) REVERT: D 435 MET cc_start: 0.7918 (mtm) cc_final: 0.7692 (mtp) REVERT: D 436 LYS cc_start: 0.7721 (tttm) cc_final: 0.7443 (mtpp) REVERT: D 441 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7117 (mt-10) REVERT: D 443 GLN cc_start: 0.7392 (tt0) cc_final: 0.7135 (tt0) REVERT: D 448 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8344 (m) REVERT: D 465 SER cc_start: 0.8284 (m) cc_final: 0.7765 (p) REVERT: D 475 SER cc_start: 0.8657 (m) cc_final: 0.8262 (p) REVERT: D 511 GLN cc_start: 0.7330 (mp10) cc_final: 0.6733 (mp10) REVERT: E 14 TRP cc_start: 0.6962 (m100) cc_final: 0.6711 (m100) REVERT: E 26 LYS cc_start: 0.8306 (mttt) cc_final: 0.8069 (mttt) REVERT: E 159 ARG cc_start: 0.7728 (mtt90) cc_final: 0.7158 (mtm-85) REVERT: E 161 ASP cc_start: 0.7722 (t0) cc_final: 0.7310 (t0) REVERT: E 166 ARG cc_start: 0.7094 (ttt180) cc_final: 0.6868 (ttt-90) REVERT: E 181 ASN cc_start: 0.8184 (m-40) cc_final: 0.7851 (m-40) REVERT: E 182 PHE cc_start: 0.8051 (m-80) cc_final: 0.7836 (m-80) REVERT: E 273 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.6743 (mmm) REVERT: E 275 LYS cc_start: 0.8463 (mmmm) cc_final: 0.8196 (tttp) REVERT: E 423 ASN cc_start: 0.8096 (t0) cc_final: 0.7834 (t0) REVERT: E 458 ASP cc_start: 0.7601 (m-30) cc_final: 0.7210 (m-30) REVERT: E 462 MET cc_start: 0.6991 (tmm) cc_final: 0.6709 (tmm) REVERT: E 479 ILE cc_start: 0.7610 (mt) cc_final: 0.7339 (tt) REVERT: E 480 LEU cc_start: 0.7570 (mt) cc_final: 0.7322 (tt) REVERT: E 504 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: E 509 ASP cc_start: 0.7874 (p0) cc_final: 0.7646 (p0) REVERT: E 531 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6557 (tt0) REVERT: E 538 GLN cc_start: 0.8173 (tt0) cc_final: 0.7728 (tt0) REVERT: E 539 ASN cc_start: 0.7878 (m-40) cc_final: 0.7434 (m-40) REVERT: G 103 ASP cc_start: 0.7312 (m-30) cc_final: 0.6452 (m-30) REVERT: G 168 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8316 (p) REVERT: G 173 ARG cc_start: 0.7374 (ttt90) cc_final: 0.6910 (ttt-90) REVERT: G 284 ARG cc_start: 0.6637 (ttt90) cc_final: 0.6248 (ttt180) REVERT: G 285 PHE cc_start: 0.7328 (p90) cc_final: 0.7095 (p90) REVERT: G 298 PHE cc_start: 0.7976 (t80) cc_final: 0.7754 (t80) REVERT: G 301 ASP cc_start: 0.7529 (t0) cc_final: 0.7252 (t70) REVERT: G 311 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7330 (ttmt) REVERT: G 409 ARG cc_start: 0.7308 (ptp-170) cc_final: 0.7075 (ptp-170) REVERT: G 428 VAL cc_start: 0.7958 (t) cc_final: 0.7604 (m) REVERT: G 474 GLU cc_start: 0.7552 (tt0) cc_final: 0.7259 (tt0) REVERT: C 26 ARG cc_start: 0.6999 (ptt90) cc_final: 0.6758 (ptt90) REVERT: C 44 ASN cc_start: 0.7908 (m110) cc_final: 0.7558 (t0) REVERT: C 60 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7535 (mp0) REVERT: C 66 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7198 (mtp85) REVERT: C 75 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8077 (pt) REVERT: C 142 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7246 (mm-40) REVERT: C 175 ASN cc_start: 0.8105 (t0) cc_final: 0.7821 (m-40) REVERT: C 177 GLU cc_start: 0.7771 (tt0) cc_final: 0.7433 (pt0) REVERT: C 224 LYS cc_start: 0.8373 (tttt) cc_final: 0.7967 (tttt) REVERT: C 236 GLU cc_start: 0.7078 (mp0) cc_final: 0.6862 (mp0) REVERT: C 304 GLN cc_start: 0.7453 (mt0) cc_final: 0.7171 (tm-30) REVERT: C 352 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7820 (mp0) REVERT: C 417 LEU cc_start: 0.8130 (mp) cc_final: 0.7859 (mt) REVERT: C 426 TYR cc_start: 0.7758 (t80) cc_final: 0.7470 (t80) REVERT: C 478 ASP cc_start: 0.7282 (m-30) cc_final: 0.6876 (m-30) REVERT: C 487 TRP cc_start: 0.6985 (OUTLIER) cc_final: 0.6248 (m-10) REVERT: C 495 LYS cc_start: 0.7841 (mttm) cc_final: 0.7178 (mttm) REVERT: C 497 ARG cc_start: 0.6786 (ptt180) cc_final: 0.6446 (ptt180) REVERT: C 517 THR cc_start: 0.8016 (m) cc_final: 0.7652 (t) REVERT: C 535 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7142 (mm-30) REVERT: C 561 GLN cc_start: 0.6170 (tp40) cc_final: 0.5940 (tp40) REVERT: C 590 ARG cc_start: 0.7547 (ttm170) cc_final: 0.7007 (ttt180) REVERT: C 606 LYS cc_start: 0.8376 (tttt) cc_final: 0.8101 (ttpp) REVERT: C 615 MET cc_start: 0.3596 (mtt) cc_final: 0.2848 (mtt) REVERT: C 631 GLU cc_start: 0.6627 (tm-30) cc_final: 0.5844 (tm-30) REVERT: C 632 LYS cc_start: 0.8035 (pttt) cc_final: 0.7740 (pttt) REVERT: B 23 GLN cc_start: 0.8076 (pt0) cc_final: 0.7613 (pt0) REVERT: B 27 ARG cc_start: 0.7995 (mtt90) cc_final: 0.7772 (mtt90) REVERT: B 37 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7284 (mm-30) REVERT: B 53 ASN cc_start: 0.7968 (m110) cc_final: 0.7632 (m-40) REVERT: B 122 LYS cc_start: 0.8269 (mttt) cc_final: 0.7918 (mmtm) REVERT: B 124 ARG cc_start: 0.7672 (ttt-90) cc_final: 0.7401 (ptm-80) REVERT: B 198 LYS cc_start: 0.8214 (ptpt) cc_final: 0.7879 (ptpt) REVERT: B 226 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6595 (tp30) REVERT: B 228 ASP cc_start: 0.7806 (t0) cc_final: 0.7433 (m-30) REVERT: B 235 LYS cc_start: 0.8073 (mtmm) cc_final: 0.7649 (mmtm) REVERT: B 243 ASN cc_start: 0.7823 (p0) cc_final: 0.7339 (t0) REVERT: B 283 GLN cc_start: 0.7612 (tt0) cc_final: 0.6881 (tm-30) REVERT: B 319 LYS cc_start: 0.8347 (tttp) cc_final: 0.7959 (ttmm) REVERT: B 358 TYR cc_start: 0.8410 (t80) cc_final: 0.8165 (t80) REVERT: B 359 GLN cc_start: 0.8299 (tt0) cc_final: 0.8075 (mt0) REVERT: B 364 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7195 (mp0) REVERT: B 366 LYS cc_start: 0.8213 (mptt) cc_final: 0.7790 (mptt) REVERT: B 454 SER cc_start: 0.6199 (OUTLIER) cc_final: 0.5345 (p) REVERT: B 532 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6954 (tm-30) REVERT: B 562 ARG cc_start: 0.7647 (ptm160) cc_final: 0.7050 (ptm160) REVERT: B 566 ARG cc_start: 0.5917 (ptt90) cc_final: 0.4684 (ptt90) REVERT: B 584 LYS cc_start: 0.8377 (mtpt) cc_final: 0.7906 (mtpt) REVERT: B 610 LYS cc_start: 0.7906 (mtmt) cc_final: 0.7517 (mmmt) REVERT: B 639 GLN cc_start: 0.6298 (pm20) cc_final: 0.6044 (pp30) REVERT: B 663 PHE cc_start: 0.6946 (m-10) cc_final: 0.6697 (m-10) REVERT: B 666 LEU cc_start: 0.7506 (mt) cc_final: 0.7249 (mm) REVERT: B 685 LYS cc_start: 0.8391 (tmtt) cc_final: 0.8091 (tmtt) REVERT: B 723 TYR cc_start: 0.3038 (OUTLIER) cc_final: -0.0790 (m-80) REVERT: B 726 GLN cc_start: 0.6817 (mt0) cc_final: 0.6187 (mp10) REVERT: H 127 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7066 (mt-10) REVERT: H 128 GLU cc_start: 0.7636 (pt0) cc_final: 0.7143 (pt0) REVERT: H 152 ASP cc_start: 0.8352 (t0) cc_final: 0.8005 (t0) REVERT: H 164 ARG cc_start: 0.5175 (OUTLIER) cc_final: 0.4860 (ptt90) REVERT: H 291 ASP cc_start: 0.7341 (t0) cc_final: 0.7041 (t0) REVERT: H 409 ARG cc_start: 0.7130 (mtp180) cc_final: 0.6796 (mtp-110) REVERT: H 418 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6877 (mt-10) REVERT: H 448 ILE cc_start: 0.7842 (mt) cc_final: 0.7445 (mp) REVERT: H 479 ASP cc_start: 0.7900 (t70) cc_final: 0.7626 (t70) REVERT: H 480 TYR cc_start: 0.7022 (OUTLIER) cc_final: 0.6415 (m-80) REVERT: H 484 PHE cc_start: 0.6460 (m-80) cc_final: 0.6015 (m-80) REVERT: F 51 GLU cc_start: 0.7268 (mm-30) cc_final: 0.7042 (mm-30) REVERT: F 158 GLN cc_start: 0.8168 (mt0) cc_final: 0.7503 (tt0) REVERT: A 4 THR cc_start: 0.8190 (p) cc_final: 0.7972 (t) REVERT: A 24 GLN cc_start: 0.7142 (tp40) cc_final: 0.6688 (tp40) REVERT: A 30 GLU cc_start: 0.7838 (tt0) cc_final: 0.7392 (tm-30) REVERT: A 170 PHE cc_start: 0.7301 (t80) cc_final: 0.6752 (t80) REVERT: A 188 LYS cc_start: 0.7182 (ttmt) cc_final: 0.6848 (ttpp) REVERT: A 216 GLU cc_start: 0.8251 (tp30) cc_final: 0.8036 (tp30) REVERT: A 225 PHE cc_start: 0.7214 (t80) cc_final: 0.6644 (t80) REVERT: A 249 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8204 (tp) REVERT: A 286 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7530 (tp30) REVERT: A 371 THR cc_start: 0.8510 (t) cc_final: 0.8299 (t) REVERT: A 382 GLU cc_start: 0.7419 (pt0) cc_final: 0.7124 (pt0) REVERT: A 394 ARG cc_start: 0.6838 (mtp85) cc_final: 0.6345 (mtp85) REVERT: A 418 LYS cc_start: 0.8322 (ptpt) cc_final: 0.8082 (ttpp) REVERT: A 450 ASP cc_start: 0.7870 (t0) cc_final: 0.7448 (t0) REVERT: A 451 TRP cc_start: 0.8007 (t-100) cc_final: 0.7621 (t60) REVERT: A 452 THR cc_start: 0.5451 (OUTLIER) cc_final: 0.5201 (p) REVERT: A 462 GLU cc_start: 0.7759 (pt0) cc_final: 0.7465 (pt0) REVERT: A 524 VAL cc_start: 0.8364 (t) cc_final: 0.8100 (m) REVERT: A 539 ASP cc_start: 0.8068 (t0) cc_final: 0.7538 (t0) REVERT: A 755 TRP cc_start: 0.8267 (p-90) cc_final: 0.7979 (p-90) REVERT: A 784 VAL cc_start: 0.8580 (t) cc_final: 0.8245 (m) REVERT: A 800 LYS cc_start: 0.8310 (mtmt) cc_final: 0.7848 (mttt) REVERT: A 803 LYS cc_start: 0.7823 (pttt) cc_final: 0.7593 (mtmm) REVERT: A 822 GLN cc_start: 0.7571 (mp10) cc_final: 0.7289 (mm-40) REVERT: A 840 LYS cc_start: 0.7345 (mmmt) cc_final: 0.7059 (mmmt) REVERT: A 881 THR cc_start: 0.8089 (p) cc_final: 0.7812 (t) REVERT: A 895 SER cc_start: 0.6679 (m) cc_final: 0.6246 (p) REVERT: A 938 ARG cc_start: 0.8705 (mtp-110) cc_final: 0.8470 (mtp-110) REVERT: A 961 VAL cc_start: 0.8134 (p) cc_final: 0.7774 (t) REVERT: A 962 LYS cc_start: 0.7257 (mmmm) cc_final: 0.6927 (mmmm) REVERT: A 993 GLU cc_start: 0.6837 (tt0) cc_final: 0.6595 (pt0) REVERT: A 1026 LYS cc_start: 0.8498 (ttmt) cc_final: 0.8216 (mtpp) REVERT: A 1032 LYS cc_start: 0.8594 (tptt) cc_final: 0.8296 (mptt) REVERT: A 1060 LEU cc_start: 0.8236 (tp) cc_final: 0.7694 (tt) REVERT: A 1151 ILE cc_start: 0.8299 (mt) cc_final: 0.7980 (mt) REVERT: A 1197 GLU cc_start: 0.7798 (tp30) cc_final: 0.7303 (tp30) REVERT: A 1228 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7320 (tpt90) REVERT: A 1239 THR cc_start: 0.6768 (m) cc_final: 0.6371 (p) REVERT: A 1273 ILE cc_start: 0.8095 (mt) cc_final: 0.7757 (mm) REVERT: A 1277 GLU cc_start: 0.7522 (tp30) cc_final: 0.6994 (tp30) REVERT: A 1307 ASN cc_start: 0.8158 (p0) cc_final: 0.7210 (p0) REVERT: A 1309 LYS cc_start: 0.8084 (mmmm) cc_final: 0.7835 (mmmt) REVERT: A 1342 HIS cc_start: 0.7232 (m-70) cc_final: 0.6652 (m-70) outliers start: 141 outliers final: 85 residues processed: 1079 average time/residue: 0.2668 time to fit residues: 452.7306 Evaluate side-chains 1070 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 970 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 261 ARG Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 392 ARG Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 513 PHE Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 666 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 547 TRP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 683 CYS Chi-restraints excluded: chain B residue 723 TYR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 480 TYR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1286 VAL Chi-restraints excluded: chain A residue 1344 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 56 optimal weight: 0.0470 chunk 289 optimal weight: 5.9990 chunk 396 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 335 optimal weight: 0.5980 chunk 214 optimal weight: 50.0000 chunk 488 optimal weight: 30.0000 chunk 286 optimal weight: 0.7980 chunk 148 optimal weight: 0.2980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 457 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 GLN E 432 GLN E 435 HIS G 177 ASN C 18 ASN C 128 GLN ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN F 173 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN A 782 GLN ** A 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS A1184 HIS A1348 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.173503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.141047 restraints weight = 60274.345| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 3.00 r_work: 0.3716 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 39343 Z= 0.128 Angle : 0.634 11.354 53371 Z= 0.326 Chirality : 0.044 0.313 5851 Planarity : 0.005 0.085 6944 Dihedral : 7.603 113.578 5768 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.89 % Allowed : 18.60 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.12), residues: 4890 helix: 0.43 (0.19), residues: 756 sheet: 0.07 (0.13), residues: 1423 loop : -0.77 (0.12), residues: 2711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 126 TYR 0.016 0.001 TYR A 41 PHE 0.027 0.001 PHE C 649 TRP 0.042 0.002 TRP D 494 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00284 (39230) covalent geometry : angle 0.62686 (53146) SS BOND : bond 0.00297 ( 93) SS BOND : angle 1.37133 ( 186) hydrogen bonds : bond 0.03595 ( 1212) hydrogen bonds : angle 5.26785 ( 3255) Misc. bond : bond 0.00072 ( 7) link_ALPHA1-2 : bond 0.00724 ( 1) link_ALPHA1-2 : angle 1.32854 ( 3) link_ALPHA1-3 : bond 0.00885 ( 1) link_ALPHA1-3 : angle 2.23441 ( 3) link_BETA1-4 : bond 0.00348 ( 5) link_BETA1-4 : angle 1.85151 ( 15) link_NAG-ASN : bond 0.00587 ( 6) link_NAG-ASN : angle 2.94853 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 976 time to evaluate : 1.082 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: symmetry clash REVERT: D 32 TYR cc_start: 0.7220 (p90) cc_final: 0.6482 (p90) REVERT: D 52 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6353 (mm-30) REVERT: D 97 ASP cc_start: 0.6906 (p0) cc_final: 0.6685 (p0) REVERT: D 120 SER cc_start: 0.7844 (m) cc_final: 0.7577 (t) REVERT: D 140 ARG cc_start: 0.7418 (mtm180) cc_final: 0.7132 (mmm160) REVERT: D 187 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6864 (mt-10) REVERT: D 253 LYS cc_start: 0.7550 (mtmt) cc_final: 0.7080 (mtpt) REVERT: D 293 GLU cc_start: 0.6775 (tt0) cc_final: 0.6228 (tt0) REVERT: D 306 MET cc_start: 0.7935 (tmm) cc_final: 0.7451 (tmm) REVERT: D 372 LEU cc_start: 0.8322 (tp) cc_final: 0.7682 (tt) REVERT: D 374 ARG cc_start: 0.7948 (mmt180) cc_final: 0.7735 (mpt-90) REVERT: D 391 THR cc_start: 0.8296 (m) cc_final: 0.8001 (p) REVERT: D 412 LYS cc_start: 0.7939 (mtmm) cc_final: 0.7718 (mtmm) REVERT: D 429 SER cc_start: 0.8470 (m) cc_final: 0.8057 (t) REVERT: D 435 MET cc_start: 0.7915 (mtm) cc_final: 0.7670 (mtp) REVERT: D 436 LYS cc_start: 0.7702 (tttm) cc_final: 0.7432 (mtpp) REVERT: D 441 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7110 (mt-10) REVERT: D 443 GLN cc_start: 0.7373 (tt0) cc_final: 0.6984 (mt0) REVERT: D 448 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8278 (m) REVERT: D 465 SER cc_start: 0.8291 (m) cc_final: 0.7829 (p) REVERT: D 475 SER cc_start: 0.8673 (m) cc_final: 0.8275 (p) REVERT: D 511 GLN cc_start: 0.7258 (mp10) cc_final: 0.6768 (mp10) REVERT: D 533 THR cc_start: 0.7800 (m) cc_final: 0.7433 (p) REVERT: E 26 LYS cc_start: 0.8298 (mttt) cc_final: 0.8042 (mttt) REVERT: E 157 GLU cc_start: 0.7210 (tt0) cc_final: 0.6837 (tt0) REVERT: E 159 ARG cc_start: 0.7728 (mtt90) cc_final: 0.7335 (mtt90) REVERT: E 161 ASP cc_start: 0.7703 (t0) cc_final: 0.7303 (t0) REVERT: E 181 ASN cc_start: 0.8235 (m-40) cc_final: 0.7888 (m-40) REVERT: E 267 GLN cc_start: 0.8077 (mt0) cc_final: 0.7375 (tt0) REVERT: E 273 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.6727 (mmm) REVERT: E 275 LYS cc_start: 0.8435 (mmmm) cc_final: 0.7915 (ttmm) REVERT: E 418 ARG cc_start: 0.7367 (ttp-110) cc_final: 0.6873 (mtp85) REVERT: E 423 ASN cc_start: 0.8124 (t0) cc_final: 0.7846 (t0) REVERT: E 462 MET cc_start: 0.7005 (tmm) cc_final: 0.6704 (tmm) REVERT: E 479 ILE cc_start: 0.7608 (mt) cc_final: 0.7309 (tt) REVERT: E 480 LEU cc_start: 0.7578 (mt) cc_final: 0.7354 (tt) REVERT: E 504 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7575 (tt0) REVERT: E 531 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6538 (tt0) REVERT: E 538 GLN cc_start: 0.8138 (tt0) cc_final: 0.7860 (tt0) REVERT: G 103 ASP cc_start: 0.7328 (m-30) cc_final: 0.6478 (m-30) REVERT: G 109 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.4647 (m-30) REVERT: G 168 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8319 (p) REVERT: G 173 ARG cc_start: 0.7385 (ttt90) cc_final: 0.6923 (ttt-90) REVERT: G 176 TRP cc_start: 0.7543 (t-100) cc_final: 0.6959 (t-100) REVERT: G 301 ASP cc_start: 0.7576 (t0) cc_final: 0.7287 (t70) REVERT: G 311 LYS cc_start: 0.7524 (ttmt) cc_final: 0.7301 (ttmt) REVERT: G 409 ARG cc_start: 0.7279 (ptp-170) cc_final: 0.7061 (ptp-170) REVERT: G 428 VAL cc_start: 0.7900 (t) cc_final: 0.7509 (m) REVERT: G 474 GLU cc_start: 0.7548 (tt0) cc_final: 0.7245 (tt0) REVERT: G 480 TYR cc_start: 0.7542 (t80) cc_final: 0.7201 (t80) REVERT: C 26 ARG cc_start: 0.7010 (ptt90) cc_final: 0.6809 (ptt90) REVERT: C 44 ASN cc_start: 0.7921 (m110) cc_final: 0.7623 (t0) REVERT: C 60 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7553 (mp0) REVERT: C 61 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6589 (tm-30) REVERT: C 66 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7217 (mtp85) REVERT: C 75 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8021 (pt) REVERT: C 142 GLN cc_start: 0.7393 (mm-40) cc_final: 0.6907 (mm-40) REVERT: C 175 ASN cc_start: 0.8045 (t0) cc_final: 0.7787 (m-40) REVERT: C 176 TYR cc_start: 0.6967 (m-80) cc_final: 0.6743 (m-80) REVERT: C 224 LYS cc_start: 0.8383 (tttt) cc_final: 0.7978 (tttt) REVERT: C 236 GLU cc_start: 0.7124 (mp0) cc_final: 0.6782 (mp0) REVERT: C 252 GLU cc_start: 0.7429 (tp30) cc_final: 0.7045 (mm-30) REVERT: C 256 LYS cc_start: 0.7830 (mttm) cc_final: 0.7607 (mttp) REVERT: C 303 LYS cc_start: 0.7875 (tttt) cc_final: 0.7120 (mtpp) REVERT: C 304 GLN cc_start: 0.7548 (mt0) cc_final: 0.7180 (tm-30) REVERT: C 352 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7797 (mp0) REVERT: C 426 TYR cc_start: 0.7838 (t80) cc_final: 0.7371 (t80) REVERT: C 436 ARG cc_start: 0.7497 (mtm-85) cc_final: 0.7174 (mtm-85) REVERT: C 478 ASP cc_start: 0.7284 (m-30) cc_final: 0.6900 (m-30) REVERT: C 487 TRP cc_start: 0.7020 (OUTLIER) cc_final: 0.6100 (m-10) REVERT: C 495 LYS cc_start: 0.7775 (mttm) cc_final: 0.7185 (mttm) REVERT: C 497 ARG cc_start: 0.6655 (ptt180) cc_final: 0.6265 (ptt180) REVERT: C 535 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7160 (mm-30) REVERT: C 602 MET cc_start: 0.7478 (ptt) cc_final: 0.7185 (ptp) REVERT: C 606 LYS cc_start: 0.8366 (tttt) cc_final: 0.8088 (ttpp) REVERT: C 631 GLU cc_start: 0.6637 (tm-30) cc_final: 0.5836 (tm-30) REVERT: C 632 LYS cc_start: 0.8022 (pttt) cc_final: 0.7705 (pttt) REVERT: B 23 GLN cc_start: 0.8070 (pt0) cc_final: 0.7574 (pt0) REVERT: B 27 ARG cc_start: 0.7987 (mtt90) cc_final: 0.7756 (mtt90) REVERT: B 37 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7220 (mm-30) REVERT: B 53 ASN cc_start: 0.7941 (m110) cc_final: 0.7594 (m-40) REVERT: B 122 LYS cc_start: 0.8211 (mttt) cc_final: 0.7941 (mmtm) REVERT: B 124 ARG cc_start: 0.7682 (ttt-90) cc_final: 0.7414 (ptm-80) REVERT: B 182 GLU cc_start: 0.7814 (pt0) cc_final: 0.7576 (pt0) REVERT: B 198 LYS cc_start: 0.8244 (ptpt) cc_final: 0.7892 (ptpt) REVERT: B 226 GLU cc_start: 0.6974 (tm-30) cc_final: 0.6381 (tp30) REVERT: B 228 ASP cc_start: 0.7822 (t0) cc_final: 0.7426 (m-30) REVERT: B 235 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7640 (mmtm) REVERT: B 243 ASN cc_start: 0.7829 (p0) cc_final: 0.7350 (t0) REVERT: B 319 LYS cc_start: 0.8321 (tttp) cc_final: 0.8007 (ttpp) REVERT: B 358 TYR cc_start: 0.8405 (t80) cc_final: 0.8132 (t80) REVERT: B 364 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7190 (mp0) REVERT: B 366 LYS cc_start: 0.8188 (mptt) cc_final: 0.7789 (mptt) REVERT: B 454 SER cc_start: 0.6175 (OUTLIER) cc_final: 0.5333 (p) REVERT: B 532 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6739 (tm-30) REVERT: B 566 ARG cc_start: 0.5887 (ptt90) cc_final: 0.4659 (ptt90) REVERT: B 584 LYS cc_start: 0.8390 (mtpt) cc_final: 0.7932 (mtpt) REVERT: B 610 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7550 (mmmt) REVERT: B 639 GLN cc_start: 0.6311 (pm20) cc_final: 0.6070 (pp30) REVERT: B 663 PHE cc_start: 0.6956 (m-10) cc_final: 0.6655 (m-10) REVERT: B 666 LEU cc_start: 0.7464 (mt) cc_final: 0.7215 (mm) REVERT: B 685 LYS cc_start: 0.8404 (tmtt) cc_final: 0.8134 (tmtt) REVERT: B 723 TYR cc_start: 0.2825 (OUTLIER) cc_final: -0.1007 (m-80) REVERT: B 726 GLN cc_start: 0.6556 (mt0) cc_final: 0.5875 (pm20) REVERT: H 127 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7065 (mt-10) REVERT: H 128 GLU cc_start: 0.7668 (pt0) cc_final: 0.7154 (pt0) REVERT: H 152 ASP cc_start: 0.8367 (t0) cc_final: 0.8026 (t0) REVERT: H 164 ARG cc_start: 0.5112 (OUTLIER) cc_final: 0.4813 (ptt90) REVERT: H 291 ASP cc_start: 0.7347 (t0) cc_final: 0.7053 (t0) REVERT: H 300 ASP cc_start: 0.7662 (m-30) cc_final: 0.7339 (m-30) REVERT: H 409 ARG cc_start: 0.7103 (mtp180) cc_final: 0.6745 (mtp-110) REVERT: H 418 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6945 (mt-10) REVERT: H 434 PHE cc_start: 0.7078 (m-80) cc_final: 0.6748 (m-10) REVERT: H 448 ILE cc_start: 0.7866 (mt) cc_final: 0.7471 (mp) REVERT: H 479 ASP cc_start: 0.7926 (t70) cc_final: 0.7630 (t70) REVERT: F 158 GLN cc_start: 0.8170 (mt0) cc_final: 0.7515 (tt0) REVERT: F 176 VAL cc_start: 0.8016 (p) cc_final: 0.7750 (m) REVERT: A 24 GLN cc_start: 0.7115 (tp40) cc_final: 0.6666 (tp40) REVERT: A 30 GLU cc_start: 0.7870 (tt0) cc_final: 0.7429 (tm-30) REVERT: A 170 PHE cc_start: 0.7290 (t80) cc_final: 0.6651 (t80) REVERT: A 188 LYS cc_start: 0.7166 (ttmt) cc_final: 0.6829 (ttpp) REVERT: A 200 GLU cc_start: 0.7763 (tt0) cc_final: 0.7542 (tt0) REVERT: A 216 GLU cc_start: 0.8303 (tp30) cc_final: 0.8087 (tp30) REVERT: A 225 PHE cc_start: 0.7263 (t80) cc_final: 0.6660 (t80) REVERT: A 249 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8174 (tp) REVERT: A 286 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7517 (tp30) REVERT: A 382 GLU cc_start: 0.7390 (pt0) cc_final: 0.7093 (pt0) REVERT: A 394 ARG cc_start: 0.6896 (mtp85) cc_final: 0.6393 (mtp85) REVERT: A 415 PHE cc_start: 0.8350 (p90) cc_final: 0.7939 (p90) REVERT: A 418 LYS cc_start: 0.8263 (ptpt) cc_final: 0.8021 (ttpp) REVERT: A 450 ASP cc_start: 0.7850 (t0) cc_final: 0.7629 (m-30) REVERT: A 451 TRP cc_start: 0.7974 (t-100) cc_final: 0.7545 (t60) REVERT: A 462 GLU cc_start: 0.7751 (pt0) cc_final: 0.7384 (pt0) REVERT: A 539 ASP cc_start: 0.7997 (t0) cc_final: 0.7488 (t0) REVERT: A 554 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7060 (mp10) REVERT: A 755 TRP cc_start: 0.8348 (p-90) cc_final: 0.7927 (p-90) REVERT: A 784 VAL cc_start: 0.8539 (t) cc_final: 0.8209 (m) REVERT: A 800 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7858 (mttt) REVERT: A 803 LYS cc_start: 0.7836 (pttt) cc_final: 0.7587 (mtmm) REVERT: A 822 GLN cc_start: 0.7623 (mp10) cc_final: 0.7340 (mm-40) REVERT: A 839 VAL cc_start: 0.7657 (OUTLIER) cc_final: 0.7148 (m) REVERT: A 840 LYS cc_start: 0.7343 (mmmt) cc_final: 0.6934 (mmmt) REVERT: A 881 THR cc_start: 0.8140 (p) cc_final: 0.7829 (t) REVERT: A 886 GLU cc_start: 0.8368 (tt0) cc_final: 0.7859 (mt-10) REVERT: A 895 SER cc_start: 0.6610 (m) cc_final: 0.6137 (p) REVERT: A 961 VAL cc_start: 0.8083 (p) cc_final: 0.7745 (t) REVERT: A 962 LYS cc_start: 0.7223 (mmmm) cc_final: 0.6892 (mmmm) REVERT: A 1026 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8215 (mtpp) REVERT: A 1032 LYS cc_start: 0.8605 (tptt) cc_final: 0.8376 (mptt) REVERT: A 1042 ARG cc_start: 0.7427 (ttt-90) cc_final: 0.7205 (ttt-90) REVERT: A 1060 LEU cc_start: 0.8234 (tp) cc_final: 0.7674 (tt) REVERT: A 1079 GLN cc_start: 0.8389 (mp10) cc_final: 0.8010 (mp10) REVERT: A 1151 ILE cc_start: 0.8338 (mt) cc_final: 0.8025 (mt) REVERT: A 1197 GLU cc_start: 0.7769 (tp30) cc_final: 0.7220 (tp30) REVERT: A 1273 ILE cc_start: 0.8105 (mt) cc_final: 0.7706 (mm) REVERT: A 1277 GLU cc_start: 0.7471 (tp30) cc_final: 0.6940 (tp30) REVERT: A 1307 ASN cc_start: 0.8149 (p0) cc_final: 0.7273 (p0) REVERT: A 1342 HIS cc_start: 0.7258 (m-70) cc_final: 0.6631 (m-70) outliers start: 159 outliers final: 99 residues processed: 1058 average time/residue: 0.2587 time to fit residues: 431.7292 Evaluate side-chains 1078 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 964 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 392 ARG Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 513 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 666 CYS Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 547 TRP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 723 TYR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain F residue 64 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1344 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 29 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 298 optimal weight: 0.9980 chunk 476 optimal weight: 50.0000 chunk 67 optimal weight: 2.9990 chunk 206 optimal weight: 50.0000 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 ASN D 457 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN E 432 GLN E 488 GLN G 177 ASN C 18 ASN C 440 ASN B 359 GLN B 367 ASN ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 ASN H 471 GLN F 78 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 HIS A 782 GLN ** A 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 ASN ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1247 ASN ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.169171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.136307 restraints weight = 60365.834| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.97 r_work: 0.3641 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.182 39343 Z= 0.320 Angle : 0.747 12.377 53371 Z= 0.391 Chirality : 0.050 0.296 5851 Planarity : 0.006 0.101 6944 Dihedral : 7.783 113.121 5768 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.11 % Allowed : 19.65 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.04 % 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: -0.94 (0.12), residues: 4890 helix: -0.02 (0.18), residues: 759 sheet: -0.17 (0.13), residues: 1441 loop : -1.03 (0.11), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 29 TYR 0.028 0.003 TYR E 413 PHE 0.031 0.003 PHE C 649 TRP 0.032 0.003 TRP A 542 HIS 0.012 0.002 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00691 (39230) covalent geometry : angle 0.73818 (53146) SS BOND : bond 0.00481 ( 93) SS BOND : angle 1.74962 ( 186) hydrogen bonds : bond 0.04521 ( 1212) hydrogen bonds : angle 5.67832 ( 3255) Misc. bond : bond 0.00077 ( 7) link_ALPHA1-2 : bond 0.00725 ( 1) link_ALPHA1-2 : angle 1.32943 ( 3) link_ALPHA1-3 : bond 0.01055 ( 1) link_ALPHA1-3 : angle 1.93805 ( 3) link_BETA1-4 : bond 0.00431 ( 5) link_BETA1-4 : angle 1.77081 ( 15) link_NAG-ASN : bond 0.00442 ( 6) link_NAG-ASN : angle 3.04082 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 983 time to evaluate : 1.478 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: D 52 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6543 (mm-30) REVERT: D 97 ASP cc_start: 0.7097 (p0) cc_final: 0.6789 (p0) REVERT: D 102 ARG cc_start: 0.8269 (ptm160) cc_final: 0.7988 (ttm-80) REVERT: D 120 SER cc_start: 0.7889 (m) cc_final: 0.7609 (t) REVERT: D 128 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: D 140 ARG cc_start: 0.7536 (mtm180) cc_final: 0.7163 (mmm160) REVERT: D 168 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7921 (mm-40) REVERT: D 187 GLU cc_start: 0.7283 (mt-10) cc_final: 0.7070 (mt-10) REVERT: D 253 LYS cc_start: 0.7708 (mtmt) cc_final: 0.7325 (mtpp) REVERT: D 273 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7404 (mm-30) REVERT: D 293 GLU cc_start: 0.6847 (tt0) cc_final: 0.6412 (tt0) REVERT: D 301 GLU cc_start: 0.8186 (tt0) cc_final: 0.7850 (tt0) REVERT: D 306 MET cc_start: 0.7995 (tmm) cc_final: 0.7443 (tmm) REVERT: D 372 LEU cc_start: 0.8401 (tp) cc_final: 0.7987 (tt) REVERT: D 391 THR cc_start: 0.8501 (m) cc_final: 0.8179 (p) REVERT: D 435 MET cc_start: 0.7932 (mtm) cc_final: 0.7703 (mtp) REVERT: D 436 LYS cc_start: 0.7762 (tttm) cc_final: 0.7408 (mtpp) REVERT: D 441 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7242 (mt-10) REVERT: D 443 GLN cc_start: 0.7515 (tt0) cc_final: 0.7303 (tt0) REVERT: D 465 SER cc_start: 0.8434 (m) cc_final: 0.7952 (p) REVERT: D 493 LYS cc_start: 0.7683 (tptt) cc_final: 0.7382 (mptt) REVERT: D 511 GLN cc_start: 0.7420 (mp10) cc_final: 0.7217 (mp-120) REVERT: D 533 THR cc_start: 0.7802 (m) cc_final: 0.7542 (p) REVERT: E 14 TRP cc_start: 0.7242 (m100) cc_final: 0.6801 (m100) REVERT: E 157 GLU cc_start: 0.7352 (tt0) cc_final: 0.7092 (tt0) REVERT: E 159 ARG cc_start: 0.7865 (mtt90) cc_final: 0.7604 (mtt90) REVERT: E 161 ASP cc_start: 0.7809 (t0) cc_final: 0.7328 (t0) REVERT: E 166 ARG cc_start: 0.7201 (ttt180) cc_final: 0.6595 (mtp180) REVERT: E 181 ASN cc_start: 0.8258 (m-40) cc_final: 0.7943 (m-40) REVERT: E 273 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7083 (mmm) REVERT: E 275 LYS cc_start: 0.8488 (mmmm) cc_final: 0.8250 (tttp) REVERT: E 418 ARG cc_start: 0.7502 (ttp-110) cc_final: 0.6991 (mtp85) REVERT: E 423 ASN cc_start: 0.8243 (t0) cc_final: 0.8005 (t0) REVERT: E 447 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6894 (mt-10) REVERT: E 462 MET cc_start: 0.7259 (tmm) cc_final: 0.6992 (tmm) REVERT: E 479 ILE cc_start: 0.7739 (mt) cc_final: 0.7438 (tt) REVERT: E 504 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: E 531 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6631 (tt0) REVERT: E 538 GLN cc_start: 0.8162 (tt0) cc_final: 0.7760 (tt0) REVERT: G 103 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.6954 (m-30) REVERT: G 122 ARG cc_start: 0.7519 (mmm160) cc_final: 0.7209 (mmm160) REVERT: G 145 ASP cc_start: 0.8065 (m-30) cc_final: 0.7809 (m-30) REVERT: G 168 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8421 (p) REVERT: G 173 ARG cc_start: 0.7449 (ttt90) cc_final: 0.6983 (mtp180) REVERT: G 176 TRP cc_start: 0.7640 (t-100) cc_final: 0.7026 (t-100) REVERT: G 284 ARG cc_start: 0.6774 (ttt90) cc_final: 0.6425 (ttt180) REVERT: G 301 ASP cc_start: 0.7626 (t0) cc_final: 0.7186 (t70) REVERT: G 311 LYS cc_start: 0.7822 (ttmt) cc_final: 0.7566 (ttmt) REVERT: G 409 ARG cc_start: 0.7359 (ptp-170) cc_final: 0.7133 (ptp-170) REVERT: G 474 GLU cc_start: 0.7629 (tt0) cc_final: 0.7341 (tt0) REVERT: G 480 TYR cc_start: 0.7718 (t80) cc_final: 0.7251 (t80) REVERT: C 44 ASN cc_start: 0.8080 (m110) cc_final: 0.7760 (t0) REVERT: C 60 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7708 (mp0) REVERT: C 61 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6929 (tm-30) REVERT: C 66 ARG cc_start: 0.7907 (mtp85) cc_final: 0.7234 (mtp85) REVERT: C 75 ILE cc_start: 0.8531 (pt) cc_final: 0.8112 (pt) REVERT: C 85 SER cc_start: 0.8158 (m) cc_final: 0.7935 (t) REVERT: C 142 GLN cc_start: 0.7603 (mm-40) cc_final: 0.7143 (mm-40) REVERT: C 175 ASN cc_start: 0.8222 (t0) cc_final: 0.7927 (m-40) REVERT: C 224 LYS cc_start: 0.8402 (tttt) cc_final: 0.8046 (tttt) REVERT: C 303 LYS cc_start: 0.7833 (tttt) cc_final: 0.7175 (mtpp) REVERT: C 355 ILE cc_start: 0.8652 (mt) cc_final: 0.8358 (tt) REVERT: C 386 GLU cc_start: 0.7319 (tm-30) cc_final: 0.7033 (tm-30) REVERT: C 414 VAL cc_start: 0.7760 (t) cc_final: 0.7077 (m) REVERT: C 424 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: C 478 ASP cc_start: 0.7311 (m-30) cc_final: 0.7007 (m-30) REVERT: C 487 TRP cc_start: 0.7031 (OUTLIER) cc_final: 0.6063 (m-10) REVERT: C 495 LYS cc_start: 0.7845 (mttm) cc_final: 0.7341 (mttm) REVERT: C 511 ARG cc_start: 0.8266 (ptm160) cc_final: 0.8034 (ptm160) REVERT: C 535 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: C 606 LYS cc_start: 0.8537 (tttt) cc_final: 0.8246 (ttpp) REVERT: C 631 GLU cc_start: 0.6727 (tm-30) cc_final: 0.5979 (tm-30) REVERT: C 632 LYS cc_start: 0.8070 (pttt) cc_final: 0.7751 (pttt) REVERT: B 37 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7338 (mm-30) REVERT: B 53 ASN cc_start: 0.8049 (m110) cc_final: 0.7697 (m-40) REVERT: B 54 TRP cc_start: 0.7708 (p90) cc_final: 0.6880 (p90) REVERT: B 73 ASP cc_start: 0.7516 (m-30) cc_final: 0.7050 (m-30) REVERT: B 122 LYS cc_start: 0.8280 (mttt) cc_final: 0.7953 (mmtm) REVERT: B 124 ARG cc_start: 0.7794 (ttt-90) cc_final: 0.7476 (ptm-80) REVERT: B 182 GLU cc_start: 0.7965 (pt0) cc_final: 0.7725 (pt0) REVERT: B 198 LYS cc_start: 0.8319 (ptpt) cc_final: 0.7970 (ptpt) REVERT: B 226 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6384 (tm-30) REVERT: B 235 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7748 (mmtm) REVERT: B 243 ASN cc_start: 0.7827 (p0) cc_final: 0.7473 (t0) REVERT: B 288 LYS cc_start: 0.8186 (ttmm) cc_final: 0.7905 (ttmm) REVERT: B 319 LYS cc_start: 0.8368 (tttp) cc_final: 0.7992 (ttmm) REVERT: B 364 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7275 (mp0) REVERT: B 366 LYS cc_start: 0.8276 (mptt) cc_final: 0.7775 (mmtt) REVERT: B 370 LEU cc_start: 0.7853 (mt) cc_final: 0.7651 (mt) REVERT: B 407 LYS cc_start: 0.7216 (tttt) cc_final: 0.6972 (tttm) REVERT: B 412 PHE cc_start: 0.8395 (t80) cc_final: 0.7934 (t80) REVERT: B 417 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7419 (tt0) REVERT: B 454 SER cc_start: 0.6375 (OUTLIER) cc_final: 0.5419 (p) REVERT: B 474 ARG cc_start: 0.8273 (mmm160) cc_final: 0.8028 (mtp85) REVERT: B 561 LYS cc_start: 0.7662 (mmmt) cc_final: 0.7353 (mmmm) REVERT: B 562 ARG cc_start: 0.7645 (ptm160) cc_final: 0.7144 (ptm160) REVERT: B 566 ARG cc_start: 0.6159 (ptt90) cc_final: 0.5055 (ptt90) REVERT: B 584 LYS cc_start: 0.8385 (mtpt) cc_final: 0.7905 (mtpt) REVERT: B 610 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7847 (mmmt) REVERT: B 639 GLN cc_start: 0.6653 (pm20) cc_final: 0.6443 (pp30) REVERT: B 640 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6097 (tt) REVERT: B 726 GLN cc_start: 0.6654 (mt0) cc_final: 0.6360 (pm20) REVERT: H 127 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7186 (mt-10) REVERT: H 128 GLU cc_start: 0.7663 (pt0) cc_final: 0.7156 (pt0) REVERT: H 152 ASP cc_start: 0.8488 (t0) cc_final: 0.8137 (t0) REVERT: H 164 ARG cc_start: 0.5299 (OUTLIER) cc_final: 0.5002 (ptt90) REVERT: H 189 LYS cc_start: 0.7588 (tmtt) cc_final: 0.7298 (tppp) REVERT: H 291 ASP cc_start: 0.7475 (t0) cc_final: 0.7249 (t0) REVERT: H 418 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6961 (mt-10) REVERT: H 448 ILE cc_start: 0.8099 (mt) cc_final: 0.7699 (mp) REVERT: H 479 ASP cc_start: 0.7970 (t70) cc_final: 0.7685 (t70) REVERT: H 484 PHE cc_start: 0.7030 (m-80) cc_final: 0.6315 (m-80) REVERT: F 158 GLN cc_start: 0.8116 (mt0) cc_final: 0.7624 (mt0) REVERT: F 176 VAL cc_start: 0.7917 (p) cc_final: 0.7609 (m) REVERT: A 7 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8460 (mm) REVERT: A 24 GLN cc_start: 0.7247 (tp40) cc_final: 0.6429 (tp40) REVERT: A 30 GLU cc_start: 0.7841 (tt0) cc_final: 0.7445 (tm-30) REVERT: A 45 LYS cc_start: 0.8383 (mmmt) cc_final: 0.8057 (mmtp) REVERT: A 188 LYS cc_start: 0.7313 (ttmt) cc_final: 0.6930 (ttpp) REVERT: A 200 GLU cc_start: 0.7834 (tt0) cc_final: 0.7542 (tt0) REVERT: A 216 GLU cc_start: 0.8308 (tp30) cc_final: 0.8048 (tp30) REVERT: A 223 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8271 (mmmt) REVERT: A 249 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8393 (tp) REVERT: A 300 LEU cc_start: 0.7572 (mt) cc_final: 0.6929 (tt) REVERT: A 382 GLU cc_start: 0.7426 (pt0) cc_final: 0.7096 (pt0) REVERT: A 394 ARG cc_start: 0.7040 (mtp85) cc_final: 0.6539 (mtp85) REVERT: A 418 LYS cc_start: 0.8439 (ptpt) cc_final: 0.8098 (ttpp) REVERT: A 462 GLU cc_start: 0.7794 (pt0) cc_final: 0.7404 (pt0) REVERT: A 482 ASN cc_start: 0.8197 (m110) cc_final: 0.7649 (m110) REVERT: A 539 ASP cc_start: 0.8072 (t0) cc_final: 0.7544 (t0) REVERT: A 755 TRP cc_start: 0.8514 (p-90) cc_final: 0.7926 (p-90) REVERT: A 784 VAL cc_start: 0.8588 (t) cc_final: 0.8284 (m) REVERT: A 800 LYS cc_start: 0.8363 (mtmt) cc_final: 0.7948 (mttt) REVERT: A 839 VAL cc_start: 0.7885 (OUTLIER) cc_final: 0.7610 (m) REVERT: A 840 LYS cc_start: 0.7657 (mmmt) cc_final: 0.7429 (mmmt) REVERT: A 881 THR cc_start: 0.8284 (p) cc_final: 0.8067 (t) REVERT: A 886 GLU cc_start: 0.8392 (tt0) cc_final: 0.8052 (mt-10) REVERT: A 956 LYS cc_start: 0.8014 (mttp) cc_final: 0.7741 (mttp) REVERT: A 961 VAL cc_start: 0.8229 (p) cc_final: 0.7935 (t) REVERT: A 962 LYS cc_start: 0.7411 (mmmm) cc_final: 0.7098 (mmmm) REVERT: A 1026 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8280 (mtpp) REVERT: A 1032 LYS cc_start: 0.8658 (tptt) cc_final: 0.8394 (mptt) REVERT: A 1060 LEU cc_start: 0.8569 (tp) cc_final: 0.8040 (tt) REVERT: A 1076 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6658 (tm-30) REVERT: A 1197 GLU cc_start: 0.7888 (tp30) cc_final: 0.7402 (tm-30) REVERT: A 1228 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7454 (tpt90) REVERT: A 1273 ILE cc_start: 0.8219 (mt) cc_final: 0.7976 (mm) REVERT: A 1277 GLU cc_start: 0.7625 (tp30) cc_final: 0.7119 (tp30) REVERT: A 1287 LYS cc_start: 0.8377 (mmtm) cc_final: 0.8138 (mmtt) REVERT: A 1307 ASN cc_start: 0.8102 (p0) cc_final: 0.7554 (p0) REVERT: A 1309 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7803 (mmmt) REVERT: A 1315 PHE cc_start: 0.8704 (p90) cc_final: 0.8436 (p90) outliers start: 168 outliers final: 107 residues processed: 1076 average time/residue: 0.2609 time to fit residues: 445.7417 Evaluate side-chains 1098 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 975 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 457 ASN Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 392 ARG Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 472 ASN Chi-restraints excluded: chain G residue 513 PHE Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 547 TRP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 64 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 373 ASN Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1344 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 8 optimal weight: 3.9990 chunk 355 optimal weight: 0.7980 chunk 131 optimal weight: 0.5980 chunk 331 optimal weight: 8.9990 chunk 420 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 430 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 316 optimal weight: 5.9990 chunk 466 optimal weight: 20.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 GLN G 99 ASN G 177 ASN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 GLN ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN ** A 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 GLN ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 HIS ** 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 = 0.4233 r_free = 0.4233 target = 0.167794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.135044 restraints weight = 60357.276| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.95 r_work: 0.3627 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.184 39343 Z= 0.341 Angle : 0.768 13.904 53371 Z= 0.403 Chirality : 0.050 0.280 5851 Planarity : 0.006 0.101 6944 Dihedral : 7.656 109.049 5768 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.86 % Allowed : 20.00 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.12), residues: 4890 helix: -0.21 (0.18), residues: 754 sheet: -0.43 (0.13), residues: 1464 loop : -1.20 (0.11), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 41 TYR 0.032 0.003 TYR E 413 PHE 0.025 0.003 PHE A 225 TRP 0.044 0.003 TRP E 416 HIS 0.012 0.002 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00730 (39230) covalent geometry : angle 0.75970 (53146) SS BOND : bond 0.00475 ( 93) SS BOND : angle 1.79714 ( 186) hydrogen bonds : bond 0.04627 ( 1212) hydrogen bonds : angle 5.82723 ( 3255) Misc. bond : bond 0.00077 ( 7) link_ALPHA1-2 : bond 0.00738 ( 1) link_ALPHA1-2 : angle 1.37034 ( 3) link_ALPHA1-3 : bond 0.01110 ( 1) link_ALPHA1-3 : angle 1.85329 ( 3) link_BETA1-4 : bond 0.00448 ( 5) link_BETA1-4 : angle 1.68809 ( 15) link_NAG-ASN : bond 0.00467 ( 6) link_NAG-ASN : angle 3.02149 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 996 time to evaluate : 1.323 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: D 13 LEU cc_start: 0.7923 (pt) cc_final: 0.7678 (pt) REVERT: D 52 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6546 (mm-30) REVERT: D 97 ASP cc_start: 0.7253 (p0) cc_final: 0.6951 (p0) REVERT: D 102 ARG cc_start: 0.8227 (ptm160) cc_final: 0.7922 (ttm170) REVERT: D 120 SER cc_start: 0.7918 (m) cc_final: 0.7629 (t) REVERT: D 168 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7957 (mm-40) REVERT: D 187 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7061 (mt-10) REVERT: D 253 LYS cc_start: 0.7776 (mtmt) cc_final: 0.7558 (ttmt) REVERT: D 273 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7302 (mm-30) REVERT: D 293 GLU cc_start: 0.6911 (tt0) cc_final: 0.6232 (tt0) REVERT: D 301 GLU cc_start: 0.8158 (tt0) cc_final: 0.7866 (tt0) REVERT: D 364 THR cc_start: 0.7664 (OUTLIER) cc_final: 0.7342 (p) REVERT: D 372 LEU cc_start: 0.8433 (tp) cc_final: 0.8072 (tt) REVERT: D 391 THR cc_start: 0.8502 (m) cc_final: 0.8182 (p) REVERT: D 412 LYS cc_start: 0.7909 (mtmm) cc_final: 0.7627 (mtmm) REVERT: D 435 MET cc_start: 0.7942 (mtm) cc_final: 0.7705 (mtp) REVERT: D 436 LYS cc_start: 0.7770 (tttm) cc_final: 0.7409 (mtpp) REVERT: D 441 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7323 (mt-10) REVERT: D 443 GLN cc_start: 0.7560 (tt0) cc_final: 0.7267 (tt0) REVERT: D 465 SER cc_start: 0.8464 (m) cc_final: 0.7942 (p) REVERT: D 469 CYS cc_start: 0.6260 (m) cc_final: 0.6042 (m) REVERT: D 493 LYS cc_start: 0.7761 (tptt) cc_final: 0.7459 (mptt) REVERT: D 533 THR cc_start: 0.7782 (m) cc_final: 0.7573 (p) REVERT: E 14 TRP cc_start: 0.7358 (m100) cc_final: 0.6926 (m100) REVERT: E 157 GLU cc_start: 0.7347 (tt0) cc_final: 0.7042 (tt0) REVERT: E 159 ARG cc_start: 0.7877 (mtt90) cc_final: 0.7548 (mtt90) REVERT: E 161 ASP cc_start: 0.7906 (t0) cc_final: 0.7344 (t0) REVERT: E 166 ARG cc_start: 0.7322 (ttt180) cc_final: 0.6492 (mtp180) REVERT: E 181 ASN cc_start: 0.8265 (m-40) cc_final: 0.7897 (m-40) REVERT: E 182 PHE cc_start: 0.8098 (m-80) cc_final: 0.7883 (m-10) REVERT: E 273 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7075 (mmm) REVERT: E 275 LYS cc_start: 0.8513 (mmmm) cc_final: 0.8299 (tttp) REVERT: E 418 ARG cc_start: 0.7489 (ttp-110) cc_final: 0.6991 (mtp85) REVERT: E 447 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6952 (mt-10) REVERT: E 462 MET cc_start: 0.7166 (tmm) cc_final: 0.6905 (tmm) REVERT: E 479 ILE cc_start: 0.7799 (mt) cc_final: 0.7524 (tt) REVERT: E 504 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7494 (tt0) REVERT: E 531 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6721 (tt0) REVERT: G 103 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7090 (m-30) REVERT: G 109 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.5054 (m-30) REVERT: G 122 ARG cc_start: 0.7512 (mmm160) cc_final: 0.7140 (mmm160) REVERT: G 145 ASP cc_start: 0.8051 (m-30) cc_final: 0.7773 (m-30) REVERT: G 168 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8450 (p) REVERT: G 173 ARG cc_start: 0.7477 (ttt90) cc_final: 0.7004 (mtp180) REVERT: G 176 TRP cc_start: 0.7681 (t-100) cc_final: 0.7071 (t-100) REVERT: G 284 ARG cc_start: 0.6770 (ttt90) cc_final: 0.6564 (ttt180) REVERT: G 301 ASP cc_start: 0.7597 (t0) cc_final: 0.7291 (t70) REVERT: G 311 LYS cc_start: 0.7837 (ttmt) cc_final: 0.7587 (ttmt) REVERT: G 409 ARG cc_start: 0.7321 (ptp-170) cc_final: 0.7044 (ptp-170) REVERT: G 474 GLU cc_start: 0.7634 (tt0) cc_final: 0.7344 (tt0) REVERT: G 480 TYR cc_start: 0.7717 (t80) cc_final: 0.7247 (t80) REVERT: C 44 ASN cc_start: 0.8149 (m110) cc_final: 0.7920 (t0) REVERT: C 60 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7829 (mp0) REVERT: C 61 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6456 (tm-30) REVERT: C 66 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7183 (mtp85) REVERT: C 142 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7216 (mm-40) REVERT: C 224 LYS cc_start: 0.8387 (tttt) cc_final: 0.8018 (tttt) REVERT: C 257 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7577 (mm-30) REVERT: C 292 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7880 (mtm-85) REVERT: C 303 LYS cc_start: 0.7804 (tttt) cc_final: 0.7159 (mtpp) REVERT: C 355 ILE cc_start: 0.8667 (mt) cc_final: 0.8327 (tt) REVERT: C 436 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7462 (mtm-85) REVERT: C 478 ASP cc_start: 0.7358 (m-30) cc_final: 0.7046 (m-30) REVERT: C 487 TRP cc_start: 0.7035 (OUTLIER) cc_final: 0.6269 (m-10) REVERT: C 495 LYS cc_start: 0.7871 (mttm) cc_final: 0.7363 (mttm) REVERT: C 497 ARG cc_start: 0.7017 (ptt-90) cc_final: 0.6401 (ptt180) REVERT: C 511 ARG cc_start: 0.8249 (ptm160) cc_final: 0.8032 (ptm160) REVERT: C 535 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: C 606 LYS cc_start: 0.8568 (tttt) cc_final: 0.8262 (ttpp) REVERT: C 631 GLU cc_start: 0.6760 (tm-30) cc_final: 0.6041 (tm-30) REVERT: C 632 LYS cc_start: 0.8016 (pttt) cc_final: 0.7688 (pttt) REVERT: C 638 SER cc_start: 0.6605 (OUTLIER) cc_final: 0.6041 (p) REVERT: B 24 SER cc_start: 0.8556 (p) cc_final: 0.8166 (t) REVERT: B 27 ARG cc_start: 0.8252 (mtt90) cc_final: 0.7915 (mtt90) REVERT: B 37 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7394 (mm-30) REVERT: B 53 ASN cc_start: 0.8024 (m110) cc_final: 0.7657 (m-40) REVERT: B 54 TRP cc_start: 0.7679 (p90) cc_final: 0.6829 (p90) REVERT: B 73 ASP cc_start: 0.7517 (m-30) cc_final: 0.7128 (m-30) REVERT: B 122 LYS cc_start: 0.8270 (mttt) cc_final: 0.7975 (mttm) REVERT: B 124 ARG cc_start: 0.7808 (ttt-90) cc_final: 0.7573 (ptm-80) REVERT: B 140 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7165 (mm-30) REVERT: B 198 LYS cc_start: 0.8330 (ptpt) cc_final: 0.8021 (ptpt) REVERT: B 228 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7211 (m-30) REVERT: B 235 LYS cc_start: 0.8189 (mtmm) cc_final: 0.7728 (mmtm) REVERT: B 243 ASN cc_start: 0.7835 (p0) cc_final: 0.7530 (t0) REVERT: B 288 LYS cc_start: 0.8199 (ttmm) cc_final: 0.7902 (ttmm) REVERT: B 297 LYS cc_start: 0.8602 (ttmm) cc_final: 0.8376 (ttmt) REVERT: B 319 LYS cc_start: 0.8333 (tttp) cc_final: 0.7981 (ttmm) REVERT: B 339 ASP cc_start: 0.7217 (m-30) cc_final: 0.6933 (m-30) REVERT: B 364 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7249 (mp0) REVERT: B 366 LYS cc_start: 0.8259 (mptt) cc_final: 0.7790 (mmtt) REVERT: B 370 LEU cc_start: 0.7842 (mt) cc_final: 0.7639 (mt) REVERT: B 407 LYS cc_start: 0.7227 (tttt) cc_final: 0.6968 (tttm) REVERT: B 417 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7426 (tt0) REVERT: B 454 SER cc_start: 0.6387 (OUTLIER) cc_final: 0.5446 (p) REVERT: B 562 ARG cc_start: 0.7728 (ptm160) cc_final: 0.7267 (ptm160) REVERT: B 566 ARG cc_start: 0.6091 (ptt90) cc_final: 0.4950 (ptt90) REVERT: B 584 LYS cc_start: 0.8353 (mtpt) cc_final: 0.7885 (mtpt) REVERT: B 596 GLU cc_start: 0.6919 (tp30) cc_final: 0.6446 (tm-30) REVERT: B 639 GLN cc_start: 0.6647 (pm20) cc_final: 0.6413 (pp30) REVERT: B 648 GLU cc_start: 0.7178 (pm20) cc_final: 0.6956 (pm20) REVERT: B 726 GLN cc_start: 0.6644 (mt0) cc_final: 0.6371 (pm20) REVERT: H 127 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7203 (mt-10) REVERT: H 128 GLU cc_start: 0.7657 (pt0) cc_final: 0.7173 (pt0) REVERT: H 152 ASP cc_start: 0.8518 (t0) cc_final: 0.8150 (t70) REVERT: H 164 ARG cc_start: 0.5324 (OUTLIER) cc_final: 0.5102 (ptt90) REVERT: H 291 ASP cc_start: 0.7420 (t0) cc_final: 0.7188 (t0) REVERT: H 418 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6932 (mt-10) REVERT: H 448 ILE cc_start: 0.8221 (mt) cc_final: 0.7939 (mt) REVERT: H 484 PHE cc_start: 0.6984 (m-80) cc_final: 0.6193 (m-80) REVERT: F 158 GLN cc_start: 0.8068 (mt0) cc_final: 0.7618 (mt0) REVERT: A 7 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8476 (mm) REVERT: A 24 GLN cc_start: 0.7255 (tp40) cc_final: 0.6237 (tp40) REVERT: A 30 GLU cc_start: 0.7827 (tt0) cc_final: 0.7395 (tm-30) REVERT: A 45 LYS cc_start: 0.8381 (mmmt) cc_final: 0.8079 (mmtp) REVERT: A 142 VAL cc_start: 0.8666 (p) cc_final: 0.8412 (t) REVERT: A 170 PHE cc_start: 0.7584 (t80) cc_final: 0.7133 (t80) REVERT: A 188 LYS cc_start: 0.7328 (ttmt) cc_final: 0.6953 (ttpp) REVERT: A 200 GLU cc_start: 0.7857 (tt0) cc_final: 0.7545 (tt0) REVERT: A 216 GLU cc_start: 0.8444 (tp30) cc_final: 0.8138 (tp30) REVERT: A 223 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8170 (mmmt) REVERT: A 249 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8273 (tt) REVERT: A 358 LYS cc_start: 0.8491 (mttt) cc_final: 0.8031 (mttm) REVERT: A 382 GLU cc_start: 0.7424 (pt0) cc_final: 0.7079 (pt0) REVERT: A 394 ARG cc_start: 0.7119 (mtp85) cc_final: 0.6598 (mtp85) REVERT: A 418 LYS cc_start: 0.8415 (ptpt) cc_final: 0.8092 (ttmm) REVERT: A 450 ASP cc_start: 0.7908 (m-30) cc_final: 0.7653 (m-30) REVERT: A 459 LEU cc_start: 0.7677 (mt) cc_final: 0.7153 (mt) REVERT: A 462 GLU cc_start: 0.7840 (pt0) cc_final: 0.7402 (pt0) REVERT: A 482 ASN cc_start: 0.8186 (m110) cc_final: 0.7685 (m110) REVERT: A 539 ASP cc_start: 0.8093 (t0) cc_final: 0.7535 (t0) REVERT: A 588 ASP cc_start: 0.8023 (t0) cc_final: 0.7767 (t70) REVERT: A 755 TRP cc_start: 0.8501 (p-90) cc_final: 0.7972 (p-90) REVERT: A 784 VAL cc_start: 0.8592 (t) cc_final: 0.8279 (m) REVERT: A 800 LYS cc_start: 0.8405 (mtmt) cc_final: 0.8028 (mttt) REVERT: A 839 VAL cc_start: 0.7790 (OUTLIER) cc_final: 0.7501 (m) REVERT: A 840 LYS cc_start: 0.7661 (mmmt) cc_final: 0.7394 (mmmt) REVERT: A 944 ARG cc_start: 0.8300 (mtp-110) cc_final: 0.8050 (ttm110) REVERT: A 956 LYS cc_start: 0.8033 (mttp) cc_final: 0.7755 (mttp) REVERT: A 961 VAL cc_start: 0.8160 (p) cc_final: 0.7889 (t) REVERT: A 962 LYS cc_start: 0.7571 (mmmm) cc_final: 0.7258 (mmmm) REVERT: A 1008 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7231 (mt-10) REVERT: A 1026 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8341 (mtpp) REVERT: A 1032 LYS cc_start: 0.8630 (tptt) cc_final: 0.8388 (mptt) REVERT: A 1099 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.8116 (t) REVERT: A 1167 THR cc_start: 0.7868 (m) cc_final: 0.7386 (p) REVERT: A 1197 GLU cc_start: 0.7894 (tp30) cc_final: 0.7493 (tm-30) REVERT: A 1273 ILE cc_start: 0.8144 (mt) cc_final: 0.7916 (mm) REVERT: A 1277 GLU cc_start: 0.7677 (tp30) cc_final: 0.7143 (tp30) REVERT: A 1307 ASN cc_start: 0.8194 (p0) cc_final: 0.7475 (p0) REVERT: A 1309 LYS cc_start: 0.8320 (mmmt) cc_final: 0.7789 (mmmt) outliers start: 158 outliers final: 111 residues processed: 1081 average time/residue: 0.2577 time to fit residues: 442.9826 Evaluate side-chains 1101 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 973 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 199 PHE Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 392 ARG Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 513 PHE Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 638 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 547 TRP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 64 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 373 ASN Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 1043 ASN Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1267 TYR Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1344 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 189 optimal weight: 0.7980 chunk 243 optimal weight: 9.9990 chunk 351 optimal weight: 0.0020 chunk 231 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 170 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 403 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 216 optimal weight: 20.0000 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN D 457 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 440 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 GLN F 173 GLN A 59 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN A 782 GLN A1094 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.170420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.137827 restraints weight = 60476.765| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 3.02 r_work: 0.3665 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 39343 Z= 0.188 Angle : 0.695 13.567 53371 Z= 0.360 Chirality : 0.046 0.314 5851 Planarity : 0.005 0.093 6944 Dihedral : 7.153 104.578 5767 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.25 % Allowed : 21.12 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.04 % 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: -1.04 (0.12), residues: 4890 helix: 0.07 (0.19), residues: 760 sheet: -0.33 (0.13), residues: 1449 loop : -1.09 (0.12), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 938 TYR 0.026 0.002 TYR D 141 PHE 0.027 0.002 PHE F 42 TRP 0.046 0.002 TRP E 416 HIS 0.011 0.001 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00413 (39230) covalent geometry : angle 0.68782 (53146) SS BOND : bond 0.00374 ( 93) SS BOND : angle 1.60853 ( 186) hydrogen bonds : bond 0.03959 ( 1212) hydrogen bonds : angle 5.53369 ( 3255) Misc. bond : bond 0.00056 ( 7) link_ALPHA1-2 : bond 0.00694 ( 1) link_ALPHA1-2 : angle 1.39085 ( 3) link_ALPHA1-3 : bond 0.00786 ( 1) link_ALPHA1-3 : angle 1.79227 ( 3) link_BETA1-4 : bond 0.00388 ( 5) link_BETA1-4 : angle 1.60787 ( 15) link_NAG-ASN : bond 0.00474 ( 6) link_NAG-ASN : angle 2.71330 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 980 time to evaluate : 1.489 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: D 52 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6491 (mm-30) REVERT: D 97 ASP cc_start: 0.7367 (p0) cc_final: 0.7124 (p0) REVERT: D 120 SER cc_start: 0.7930 (m) cc_final: 0.7678 (t) REVERT: D 128 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: D 141 TYR cc_start: 0.8560 (t80) cc_final: 0.8269 (t80) REVERT: D 244 ASP cc_start: 0.8266 (m-30) cc_final: 0.7945 (m-30) REVERT: D 253 LYS cc_start: 0.7715 (mtmt) cc_final: 0.7285 (mtpt) REVERT: D 273 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7288 (mm-30) REVERT: D 293 GLU cc_start: 0.6846 (tt0) cc_final: 0.6294 (tt0) REVERT: D 306 MET cc_start: 0.8106 (tmm) cc_final: 0.7402 (tmm) REVERT: D 364 THR cc_start: 0.7590 (OUTLIER) cc_final: 0.7364 (p) REVERT: D 372 LEU cc_start: 0.8391 (tp) cc_final: 0.7920 (tt) REVERT: D 391 THR cc_start: 0.8376 (m) cc_final: 0.8069 (p) REVERT: D 412 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7518 (mtmm) REVERT: D 435 MET cc_start: 0.7916 (mtm) cc_final: 0.7669 (mtp) REVERT: D 436 LYS cc_start: 0.7736 (tttm) cc_final: 0.7382 (mtpp) REVERT: D 441 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7335 (mt-10) REVERT: D 442 PHE cc_start: 0.7955 (t80) cc_final: 0.7635 (t80) REVERT: D 443 GLN cc_start: 0.7341 (tt0) cc_final: 0.6869 (mt0) REVERT: D 465 SER cc_start: 0.8406 (m) cc_final: 0.7871 (p) REVERT: D 469 CYS cc_start: 0.6241 (m) cc_final: 0.6010 (m) REVERT: D 533 THR cc_start: 0.7773 (m) cc_final: 0.7529 (p) REVERT: E 14 TRP cc_start: 0.7170 (m100) cc_final: 0.6871 (m100) REVERT: E 157 GLU cc_start: 0.7325 (tt0) cc_final: 0.7000 (tt0) REVERT: E 159 ARG cc_start: 0.7826 (mtt90) cc_final: 0.7482 (mtt90) REVERT: E 161 ASP cc_start: 0.7908 (t0) cc_final: 0.7321 (t0) REVERT: E 166 ARG cc_start: 0.7141 (ttt180) cc_final: 0.6577 (mtp180) REVERT: E 181 ASN cc_start: 0.8208 (m-40) cc_final: 0.7842 (m-40) REVERT: E 182 PHE cc_start: 0.8072 (m-80) cc_final: 0.7763 (m-10) REVERT: E 273 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.6980 (mmm) REVERT: E 275 LYS cc_start: 0.8464 (mmmm) cc_final: 0.8186 (tttp) REVERT: E 418 ARG cc_start: 0.7412 (ttp-110) cc_final: 0.6943 (mtp85) REVERT: E 447 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6876 (mt-10) REVERT: E 460 TYR cc_start: 0.7372 (t80) cc_final: 0.6966 (t80) REVERT: E 462 MET cc_start: 0.7162 (tmm) cc_final: 0.6936 (tmm) REVERT: E 479 ILE cc_start: 0.7780 (mt) cc_final: 0.7479 (tt) REVERT: E 531 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6695 (tt0) REVERT: G 103 ASP cc_start: 0.7690 (m-30) cc_final: 0.6789 (m-30) REVERT: G 109 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.4987 (m-30) REVERT: G 122 ARG cc_start: 0.7438 (mmm160) cc_final: 0.7069 (mmm160) REVERT: G 145 ASP cc_start: 0.7990 (m-30) cc_final: 0.7714 (m-30) REVERT: G 173 ARG cc_start: 0.7434 (ttt90) cc_final: 0.6843 (mtp180) REVERT: G 174 ARG cc_start: 0.7997 (ttp-110) cc_final: 0.7680 (ttp-110) REVERT: G 176 TRP cc_start: 0.7618 (t-100) cc_final: 0.7036 (t-100) REVERT: G 284 ARG cc_start: 0.6810 (ttt90) cc_final: 0.6560 (ttt180) REVERT: G 301 ASP cc_start: 0.7534 (t0) cc_final: 0.7233 (t70) REVERT: G 311 LYS cc_start: 0.7730 (ttmt) cc_final: 0.7487 (ttmt) REVERT: G 409 ARG cc_start: 0.7327 (ptp-170) cc_final: 0.6987 (ptp-170) REVERT: G 474 GLU cc_start: 0.7589 (tt0) cc_final: 0.7292 (tt0) REVERT: G 480 TYR cc_start: 0.7631 (t80) cc_final: 0.7219 (t80) REVERT: C 44 ASN cc_start: 0.8096 (m110) cc_final: 0.7887 (t0) REVERT: C 60 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7852 (mp0) REVERT: C 61 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6477 (tm-30) REVERT: C 66 ARG cc_start: 0.7881 (mtp85) cc_final: 0.7141 (mtp85) REVERT: C 142 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7232 (mm-40) REVERT: C 224 LYS cc_start: 0.8371 (tttt) cc_final: 0.8010 (tttt) REVERT: C 226 TYR cc_start: 0.7705 (t80) cc_final: 0.7238 (t80) REVERT: C 246 GLU cc_start: 0.7736 (tt0) cc_final: 0.7468 (tt0) REVERT: C 257 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7551 (mm-30) REVERT: C 303 LYS cc_start: 0.7807 (tttt) cc_final: 0.7167 (mtpp) REVERT: C 352 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7728 (mp0) REVERT: C 355 ILE cc_start: 0.8582 (mt) cc_final: 0.8249 (tt) REVERT: C 436 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.7344 (mtm-85) REVERT: C 478 ASP cc_start: 0.7339 (m-30) cc_final: 0.7029 (m-30) REVERT: C 487 TRP cc_start: 0.7008 (OUTLIER) cc_final: 0.6175 (m-10) REVERT: C 495 LYS cc_start: 0.7816 (mttm) cc_final: 0.7327 (mttm) REVERT: C 497 ARG cc_start: 0.6888 (ptt-90) cc_final: 0.6341 (ptt180) REVERT: C 511 ARG cc_start: 0.8230 (ptm160) cc_final: 0.7919 (ptm160) REVERT: C 535 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7409 (mm-30) REVERT: C 590 ARG cc_start: 0.7629 (ttm170) cc_final: 0.7347 (ttm170) REVERT: C 606 LYS cc_start: 0.8458 (tttt) cc_final: 0.8164 (ttpp) REVERT: C 631 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6021 (tm-30) REVERT: C 632 LYS cc_start: 0.7956 (pttt) cc_final: 0.7653 (pttt) REVERT: C 649 PHE cc_start: 0.6538 (m-10) cc_final: 0.6309 (m-10) REVERT: B 24 SER cc_start: 0.8496 (p) cc_final: 0.8082 (t) REVERT: B 27 ARG cc_start: 0.8226 (mtt90) cc_final: 0.7849 (mtt90) REVERT: B 37 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7336 (mm-30) REVERT: B 53 ASN cc_start: 0.7981 (m110) cc_final: 0.7554 (m-40) REVERT: B 54 TRP cc_start: 0.7617 (p90) cc_final: 0.6739 (p90) REVERT: B 65 ASP cc_start: 0.8305 (m-30) cc_final: 0.8085 (t0) REVERT: B 73 ASP cc_start: 0.7447 (m-30) cc_final: 0.7073 (m-30) REVERT: B 122 LYS cc_start: 0.8154 (mttt) cc_final: 0.7861 (mttm) REVERT: B 124 ARG cc_start: 0.7747 (ttt-90) cc_final: 0.7427 (ptm-80) REVERT: B 133 ARG cc_start: 0.8154 (tpp80) cc_final: 0.7881 (tpp80) REVERT: B 182 GLU cc_start: 0.7984 (pt0) cc_final: 0.7750 (pt0) REVERT: B 198 LYS cc_start: 0.8286 (ptpt) cc_final: 0.7956 (ptpt) REVERT: B 228 ASP cc_start: 0.7694 (m-30) cc_final: 0.7240 (m-30) REVERT: B 235 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7658 (mmtm) REVERT: B 243 ASN cc_start: 0.7805 (p0) cc_final: 0.7524 (t0) REVERT: B 288 LYS cc_start: 0.8159 (ttmm) cc_final: 0.7892 (ttmm) REVERT: B 319 LYS cc_start: 0.8340 (tttp) cc_final: 0.8009 (ttpp) REVERT: B 336 ILE cc_start: 0.7905 (mm) cc_final: 0.7586 (tt) REVERT: B 370 LEU cc_start: 0.7806 (mt) cc_final: 0.7603 (mt) REVERT: B 407 LYS cc_start: 0.7221 (tttt) cc_final: 0.6965 (tttm) REVERT: B 454 SER cc_start: 0.6313 (OUTLIER) cc_final: 0.5439 (p) REVERT: B 474 ARG cc_start: 0.8222 (mmm160) cc_final: 0.7886 (mtp85) REVERT: B 562 ARG cc_start: 0.7652 (ptm160) cc_final: 0.7141 (ptm160) REVERT: B 584 LYS cc_start: 0.8345 (mtpt) cc_final: 0.7867 (mtpt) REVERT: B 596 GLU cc_start: 0.7010 (tp30) cc_final: 0.6622 (tm-30) REVERT: B 610 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7680 (mmmt) REVERT: B 639 GLN cc_start: 0.6697 (pm20) cc_final: 0.6429 (pp30) REVERT: B 673 GLN cc_start: 0.8127 (tt0) cc_final: 0.7778 (tp40) REVERT: H 127 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7121 (mt-10) REVERT: H 128 GLU cc_start: 0.7645 (pt0) cc_final: 0.7197 (pt0) REVERT: H 152 ASP cc_start: 0.8492 (t0) cc_final: 0.8081 (t70) REVERT: H 291 ASP cc_start: 0.7435 (t0) cc_final: 0.7152 (t0) REVERT: H 418 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7069 (mt-10) REVERT: H 448 ILE cc_start: 0.8168 (mt) cc_final: 0.7794 (mp) REVERT: H 484 PHE cc_start: 0.7057 (m-80) cc_final: 0.6294 (m-80) REVERT: F 54 THR cc_start: 0.6279 (OUTLIER) cc_final: 0.6077 (t) REVERT: F 158 GLN cc_start: 0.8090 (mt0) cc_final: 0.7706 (mt0) REVERT: A 24 GLN cc_start: 0.7182 (tp40) cc_final: 0.6157 (tp40) REVERT: A 30 GLU cc_start: 0.7864 (tt0) cc_final: 0.7384 (tm-30) REVERT: A 45 LYS cc_start: 0.8332 (mmmt) cc_final: 0.8088 (mmtp) REVERT: A 94 SER cc_start: 0.8216 (OUTLIER) cc_final: 0.7980 (p) REVERT: A 188 LYS cc_start: 0.7266 (ttmt) cc_final: 0.6914 (ttpp) REVERT: A 200 GLU cc_start: 0.7831 (tt0) cc_final: 0.7598 (tt0) REVERT: A 216 GLU cc_start: 0.8438 (tp30) cc_final: 0.8160 (tp30) REVERT: A 223 LYS cc_start: 0.8477 (mmmt) cc_final: 0.8092 (mmmt) REVERT: A 249 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8351 (tp) REVERT: A 363 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7629 (mm-40) REVERT: A 382 GLU cc_start: 0.7373 (pt0) cc_final: 0.7049 (pt0) REVERT: A 394 ARG cc_start: 0.7054 (mtp85) cc_final: 0.6545 (mtp85) REVERT: A 418 LYS cc_start: 0.8376 (ptpt) cc_final: 0.8093 (ttpp) REVERT: A 450 ASP cc_start: 0.7920 (m-30) cc_final: 0.7658 (m-30) REVERT: A 459 LEU cc_start: 0.7710 (mt) cc_final: 0.7236 (mt) REVERT: A 462 GLU cc_start: 0.7884 (pt0) cc_final: 0.7400 (pt0) REVERT: A 482 ASN cc_start: 0.8182 (m110) cc_final: 0.7700 (m110) REVERT: A 539 ASP cc_start: 0.8091 (t0) cc_final: 0.7575 (t0) REVERT: A 541 VAL cc_start: 0.8821 (p) cc_final: 0.8436 (m) REVERT: A 576 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7697 (p) REVERT: A 578 MET cc_start: 0.7572 (tpp) cc_final: 0.7222 (mmt) REVERT: A 588 ASP cc_start: 0.8046 (t0) cc_final: 0.7747 (t70) REVERT: A 652 LYS cc_start: 0.8211 (ptpp) cc_final: 0.7786 (mtmm) REVERT: A 755 TRP cc_start: 0.8494 (p-90) cc_final: 0.7971 (p-90) REVERT: A 774 ASP cc_start: 0.6727 (m-30) cc_final: 0.6312 (t0) REVERT: A 784 VAL cc_start: 0.8571 (t) cc_final: 0.8258 (m) REVERT: A 800 LYS cc_start: 0.8380 (mtmt) cc_final: 0.7988 (mttt) REVERT: A 839 VAL cc_start: 0.7666 (OUTLIER) cc_final: 0.7289 (m) REVERT: A 840 LYS cc_start: 0.7483 (mmmt) cc_final: 0.7225 (mmmt) REVERT: A 881 THR cc_start: 0.8195 (m) cc_final: 0.7680 (t) REVERT: A 944 ARG cc_start: 0.8294 (mtp-110) cc_final: 0.8036 (ttm110) REVERT: A 956 LYS cc_start: 0.7924 (mttp) cc_final: 0.7640 (mttp) REVERT: A 961 VAL cc_start: 0.8181 (p) cc_final: 0.7850 (t) REVERT: A 962 LYS cc_start: 0.7419 (mmmm) cc_final: 0.7124 (mmmm) REVERT: A 991 GLU cc_start: 0.6217 (mm-30) cc_final: 0.5973 (mt-10) REVERT: A 1008 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7202 (mt-10) REVERT: A 1026 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8366 (mtpp) REVERT: A 1032 LYS cc_start: 0.8614 (tptt) cc_final: 0.8369 (mptt) REVERT: A 1099 SER cc_start: 0.8208 (OUTLIER) cc_final: 0.7958 (t) REVERT: A 1167 THR cc_start: 0.7739 (m) cc_final: 0.7201 (p) REVERT: A 1197 GLU cc_start: 0.7792 (tp30) cc_final: 0.7289 (tp30) REVERT: A 1228 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7393 (ttm-80) REVERT: A 1273 ILE cc_start: 0.8097 (mt) cc_final: 0.7866 (mm) REVERT: A 1277 GLU cc_start: 0.7585 (tp30) cc_final: 0.7082 (tp30) REVERT: A 1287 LYS cc_start: 0.8320 (mmtm) cc_final: 0.8103 (mmtt) REVERT: A 1307 ASN cc_start: 0.8220 (p0) cc_final: 0.7489 (p0) REVERT: A 1309 LYS cc_start: 0.8273 (mmmt) cc_final: 0.7854 (mmmt) REVERT: A 1348 HIS cc_start: 0.7398 (m-70) cc_final: 0.7175 (m-70) outliers start: 133 outliers final: 97 residues processed: 1050 average time/residue: 0.2587 time to fit residues: 429.8541 Evaluate side-chains 1063 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 950 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 457 ASN Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 392 ARG Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 471 GLN Chi-restraints excluded: chain G residue 513 PHE Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 547 TRP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 64 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 373 ASN Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 1043 ASN Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1286 VAL Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1344 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 458 optimal weight: 2.9990 chunk 376 optimal weight: 0.9980 chunk 203 optimal weight: 9.9990 chunk 430 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 476 optimal weight: 50.0000 chunk 8 optimal weight: 3.9990 chunk 416 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 454 optimal weight: 0.3980 chunk 261 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 457 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS F 78 GLN F 173 GLN A 59 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.170461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.137717 restraints weight = 60460.927| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.04 r_work: 0.3659 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 39343 Z= 0.156 Angle : 0.687 14.159 53371 Z= 0.353 Chirality : 0.045 0.264 5851 Planarity : 0.005 0.088 6944 Dihedral : 6.859 100.042 5767 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.86 % Allowed : 21.66 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -0.92 (0.12), residues: 4890 helix: 0.26 (0.19), residues: 757 sheet: -0.26 (0.13), residues: 1466 loop : -1.05 (0.12), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 938 TYR 0.035 0.002 TYR C 418 PHE 0.024 0.002 PHE A 415 TRP 0.048 0.002 TRP A 451 HIS 0.011 0.001 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00349 (39230) covalent geometry : angle 0.68104 (53146) SS BOND : bond 0.00286 ( 93) SS BOND : angle 1.44008 ( 186) hydrogen bonds : bond 0.03778 ( 1212) hydrogen bonds : angle 5.40379 ( 3255) Misc. bond : bond 0.00056 ( 7) link_ALPHA1-2 : bond 0.00700 ( 1) link_ALPHA1-2 : angle 1.40370 ( 3) link_ALPHA1-3 : bond 0.00910 ( 1) link_ALPHA1-3 : angle 1.72173 ( 3) link_BETA1-4 : bond 0.00371 ( 5) link_BETA1-4 : angle 1.55079 ( 15) link_NAG-ASN : bond 0.00481 ( 6) link_NAG-ASN : angle 2.60947 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 956 time to evaluate : 1.531 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: D 52 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6735 (mm-30) REVERT: D 102 ARG cc_start: 0.8290 (ptm160) cc_final: 0.7927 (ttp-170) REVERT: D 120 SER cc_start: 0.7898 (m) cc_final: 0.7606 (t) REVERT: D 141 TYR cc_start: 0.8519 (t80) cc_final: 0.8236 (t80) REVERT: D 168 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7898 (mm-40) REVERT: D 244 ASP cc_start: 0.8304 (m-30) cc_final: 0.8002 (m-30) REVERT: D 253 LYS cc_start: 0.7678 (mtmt) cc_final: 0.7268 (mtpt) REVERT: D 273 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7246 (mm-30) REVERT: D 293 GLU cc_start: 0.6920 (tt0) cc_final: 0.6344 (tt0) REVERT: D 306 MET cc_start: 0.8142 (tmm) cc_final: 0.7417 (tmm) REVERT: D 364 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7365 (p) REVERT: D 372 LEU cc_start: 0.8375 (tp) cc_final: 0.7898 (tt) REVERT: D 391 THR cc_start: 0.8296 (m) cc_final: 0.7977 (p) REVERT: D 412 LYS cc_start: 0.7815 (mtmm) cc_final: 0.7508 (mtmm) REVERT: D 429 SER cc_start: 0.8563 (m) cc_final: 0.8138 (t) REVERT: D 435 MET cc_start: 0.7933 (mtm) cc_final: 0.7680 (mtp) REVERT: D 436 LYS cc_start: 0.7720 (tttm) cc_final: 0.7359 (mtpp) REVERT: D 441 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7309 (mt-10) REVERT: D 443 GLN cc_start: 0.7330 (tt0) cc_final: 0.6909 (mt0) REVERT: D 465 SER cc_start: 0.8365 (m) cc_final: 0.7793 (p) REVERT: D 469 CYS cc_start: 0.6169 (m) cc_final: 0.5931 (m) REVERT: D 533 THR cc_start: 0.7773 (m) cc_final: 0.7526 (p) REVERT: E 157 GLU cc_start: 0.7329 (tt0) cc_final: 0.7008 (tt0) REVERT: E 159 ARG cc_start: 0.7899 (mtt90) cc_final: 0.7594 (mtt90) REVERT: E 161 ASP cc_start: 0.7821 (t0) cc_final: 0.7263 (t0) REVERT: E 166 ARG cc_start: 0.6736 (ttt180) cc_final: 0.6487 (ttt-90) REVERT: E 275 LYS cc_start: 0.8469 (mmmm) cc_final: 0.8181 (tttp) REVERT: E 418 ARG cc_start: 0.7362 (ttp-110) cc_final: 0.6901 (mtp85) REVERT: E 447 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6881 (mt-10) REVERT: E 458 ASP cc_start: 0.7630 (m-30) cc_final: 0.7214 (m-30) REVERT: E 460 TYR cc_start: 0.7328 (t80) cc_final: 0.6989 (t80) REVERT: E 462 MET cc_start: 0.7170 (tmm) cc_final: 0.6936 (tmm) REVERT: E 479 ILE cc_start: 0.7664 (mt) cc_final: 0.7388 (tt) REVERT: E 504 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: E 531 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6630 (tt0) REVERT: G 103 ASP cc_start: 0.7595 (m-30) cc_final: 0.6643 (m-30) REVERT: G 109 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.4746 (m-30) REVERT: G 145 ASP cc_start: 0.7990 (m-30) cc_final: 0.7714 (m-30) REVERT: G 173 ARG cc_start: 0.7417 (ttt90) cc_final: 0.7026 (ttt-90) REVERT: G 174 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7677 (ttp-110) REVERT: G 176 TRP cc_start: 0.7594 (t-100) cc_final: 0.7024 (t-100) REVERT: G 284 ARG cc_start: 0.6772 (ttt90) cc_final: 0.6533 (ttt180) REVERT: G 301 ASP cc_start: 0.7567 (t0) cc_final: 0.7271 (t70) REVERT: G 311 LYS cc_start: 0.7662 (ttmt) cc_final: 0.7405 (ttmt) REVERT: G 409 ARG cc_start: 0.7266 (ptp-170) cc_final: 0.6968 (ptp-170) REVERT: G 474 GLU cc_start: 0.7591 (tt0) cc_final: 0.7286 (tt0) REVERT: G 480 TYR cc_start: 0.7615 (t80) cc_final: 0.7222 (t80) REVERT: C 60 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7827 (mp0) REVERT: C 95 ASP cc_start: 0.8129 (m-30) cc_final: 0.7888 (m-30) REVERT: C 142 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7223 (mm-40) REVERT: C 224 LYS cc_start: 0.8344 (tttt) cc_final: 0.7926 (tttt) REVERT: C 246 GLU cc_start: 0.7805 (tt0) cc_final: 0.7408 (tt0) REVERT: C 303 LYS cc_start: 0.7773 (tttt) cc_final: 0.7113 (mtpp) REVERT: C 478 ASP cc_start: 0.7357 (m-30) cc_final: 0.7011 (m-30) REVERT: C 487 TRP cc_start: 0.7009 (OUTLIER) cc_final: 0.6200 (m-10) REVERT: C 495 LYS cc_start: 0.7749 (mttm) cc_final: 0.7269 (mttm) REVERT: C 497 ARG cc_start: 0.6821 (ptt-90) cc_final: 0.6319 (ptt180) REVERT: C 535 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7346 (mm-30) REVERT: C 590 ARG cc_start: 0.7568 (ttm170) cc_final: 0.7279 (ttm170) REVERT: C 606 LYS cc_start: 0.8457 (tttt) cc_final: 0.8159 (ttpp) REVERT: C 631 GLU cc_start: 0.6813 (tm-30) cc_final: 0.6157 (tm-30) REVERT: C 632 LYS cc_start: 0.7940 (pttt) cc_final: 0.7655 (pttt) REVERT: B 24 SER cc_start: 0.8444 (p) cc_final: 0.8027 (t) REVERT: B 27 ARG cc_start: 0.8214 (mtt90) cc_final: 0.7873 (mtt90) REVERT: B 37 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7318 (mm-30) REVERT: B 53 ASN cc_start: 0.7947 (m110) cc_final: 0.7518 (m-40) REVERT: B 54 TRP cc_start: 0.7591 (p90) cc_final: 0.6912 (p90) REVERT: B 65 ASP cc_start: 0.8304 (m-30) cc_final: 0.8096 (t0) REVERT: B 73 ASP cc_start: 0.7455 (m-30) cc_final: 0.7079 (m-30) REVERT: B 122 LYS cc_start: 0.8096 (mttt) cc_final: 0.7832 (mmtm) REVERT: B 124 ARG cc_start: 0.7734 (ttt-90) cc_final: 0.7423 (ptm-80) REVERT: B 158 VAL cc_start: 0.7070 (OUTLIER) cc_final: 0.6270 (t) REVERT: B 182 GLU cc_start: 0.7984 (pt0) cc_final: 0.7744 (pt0) REVERT: B 198 LYS cc_start: 0.8263 (ptpt) cc_final: 0.7930 (ptpt) REVERT: B 228 ASP cc_start: 0.7682 (m-30) cc_final: 0.7228 (m-30) REVERT: B 235 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7659 (mmtm) REVERT: B 243 ASN cc_start: 0.7759 (p0) cc_final: 0.7495 (t0) REVERT: B 288 LYS cc_start: 0.8122 (ttmm) cc_final: 0.7855 (ttmm) REVERT: B 319 LYS cc_start: 0.8304 (tttp) cc_final: 0.7930 (ttmm) REVERT: B 336 ILE cc_start: 0.7844 (mm) cc_final: 0.7512 (tt) REVERT: B 358 TYR cc_start: 0.8459 (t80) cc_final: 0.8028 (t80) REVERT: B 364 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6967 (tm-30) REVERT: B 407 LYS cc_start: 0.7174 (tttt) cc_final: 0.6925 (tttm) REVERT: B 454 SER cc_start: 0.6259 (OUTLIER) cc_final: 0.5363 (p) REVERT: B 474 ARG cc_start: 0.8208 (mmm160) cc_final: 0.7904 (mtp85) REVERT: B 532 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6343 (tm-30) REVERT: B 534 GLN cc_start: 0.7823 (mt0) cc_final: 0.7560 (mt0) REVERT: B 562 ARG cc_start: 0.7674 (ptm160) cc_final: 0.7138 (ptm160) REVERT: B 566 ARG cc_start: 0.5989 (ptt90) cc_final: 0.4716 (ptt90) REVERT: B 584 LYS cc_start: 0.8366 (mtpt) cc_final: 0.7865 (mtpt) REVERT: B 596 GLU cc_start: 0.7015 (tp30) cc_final: 0.6605 (tm-30) REVERT: B 610 LYS cc_start: 0.8027 (mtmt) cc_final: 0.7532 (mmmt) REVERT: B 639 GLN cc_start: 0.6654 (pm20) cc_final: 0.6394 (pp30) REVERT: B 673 GLN cc_start: 0.8103 (tt0) cc_final: 0.7804 (tp40) REVERT: B 726 GLN cc_start: 0.6352 (pm20) cc_final: 0.6115 (mp10) REVERT: H 127 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7177 (mt-10) REVERT: H 128 GLU cc_start: 0.7670 (pt0) cc_final: 0.7193 (pt0) REVERT: H 152 ASP cc_start: 0.8470 (t0) cc_final: 0.8115 (t0) REVERT: H 291 ASP cc_start: 0.7447 (t0) cc_final: 0.7136 (t0) REVERT: H 418 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7082 (mt-10) REVERT: H 448 ILE cc_start: 0.8123 (mt) cc_final: 0.7733 (mp) REVERT: H 479 ASP cc_start: 0.8019 (t70) cc_final: 0.7792 (t70) REVERT: H 484 PHE cc_start: 0.7081 (m-80) cc_final: 0.6284 (m-80) REVERT: F 54 THR cc_start: 0.6188 (OUTLIER) cc_final: 0.5963 (t) REVERT: F 158 GLN cc_start: 0.8053 (mt0) cc_final: 0.7634 (mt0) REVERT: A 24 GLN cc_start: 0.7194 (tp40) cc_final: 0.6469 (tp40) REVERT: A 30 GLU cc_start: 0.7868 (tt0) cc_final: 0.7377 (tm-30) REVERT: A 45 LYS cc_start: 0.8342 (mmmt) cc_final: 0.7996 (mmtp) REVERT: A 94 SER cc_start: 0.8196 (OUTLIER) cc_final: 0.7988 (p) REVERT: A 141 THR cc_start: 0.8357 (m) cc_final: 0.7934 (p) REVERT: A 188 LYS cc_start: 0.7210 (ttmt) cc_final: 0.6839 (ttpp) REVERT: A 200 GLU cc_start: 0.7862 (tt0) cc_final: 0.7611 (tt0) REVERT: A 216 GLU cc_start: 0.8408 (tp30) cc_final: 0.8128 (tp30) REVERT: A 223 LYS cc_start: 0.8462 (mmmt) cc_final: 0.8020 (mmmt) REVERT: A 249 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8278 (tp) REVERT: A 273 MET cc_start: 0.7016 (mmm) cc_final: 0.6727 (mmm) REVERT: A 363 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7688 (mm-40) REVERT: A 382 GLU cc_start: 0.7316 (pt0) cc_final: 0.6966 (pt0) REVERT: A 394 ARG cc_start: 0.7064 (mtp85) cc_final: 0.6576 (mtp85) REVERT: A 415 PHE cc_start: 0.8245 (p90) cc_final: 0.7927 (p90) REVERT: A 418 LYS cc_start: 0.8352 (ptpt) cc_final: 0.8092 (ttpp) REVERT: A 459 LEU cc_start: 0.7764 (mt) cc_final: 0.7404 (mt) REVERT: A 462 GLU cc_start: 0.7963 (pt0) cc_final: 0.7524 (pt0) REVERT: A 482 ASN cc_start: 0.8210 (m110) cc_final: 0.7696 (m110) REVERT: A 498 GLU cc_start: 0.6807 (tm-30) cc_final: 0.6557 (tm-30) REVERT: A 539 ASP cc_start: 0.8125 (t0) cc_final: 0.7604 (t0) REVERT: A 541 VAL cc_start: 0.8763 (p) cc_final: 0.8398 (m) REVERT: A 546 GLU cc_start: 0.7117 (tt0) cc_final: 0.6812 (pt0) REVERT: A 576 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7658 (p) REVERT: A 588 ASP cc_start: 0.8099 (t0) cc_final: 0.7792 (t70) REVERT: A 652 LYS cc_start: 0.8203 (ptpp) cc_final: 0.7754 (mtmm) REVERT: A 755 TRP cc_start: 0.8482 (p-90) cc_final: 0.7946 (p-90) REVERT: A 774 ASP cc_start: 0.6729 (m-30) cc_final: 0.6306 (t0) REVERT: A 784 VAL cc_start: 0.8567 (t) cc_final: 0.8220 (m) REVERT: A 800 LYS cc_start: 0.8354 (mtmt) cc_final: 0.7945 (mttt) REVERT: A 839 VAL cc_start: 0.7600 (OUTLIER) cc_final: 0.7161 (m) REVERT: A 840 LYS cc_start: 0.7446 (mmmt) cc_final: 0.7100 (mmmt) REVERT: A 895 SER cc_start: 0.6854 (m) cc_final: 0.6322 (p) REVERT: A 944 ARG cc_start: 0.8310 (mtp-110) cc_final: 0.8025 (ttm110) REVERT: A 956 LYS cc_start: 0.7897 (mttp) cc_final: 0.7623 (mttp) REVERT: A 961 VAL cc_start: 0.8029 (p) cc_final: 0.7735 (t) REVERT: A 962 LYS cc_start: 0.7388 (mmmm) cc_final: 0.7108 (mmmm) REVERT: A 1008 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7209 (mt-10) REVERT: A 1026 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8408 (mtpp) REVERT: A 1032 LYS cc_start: 0.8636 (tptt) cc_final: 0.8391 (mptt) REVERT: A 1060 LEU cc_start: 0.8179 (tp) cc_final: 0.7735 (tt) REVERT: A 1099 SER cc_start: 0.8084 (OUTLIER) cc_final: 0.7859 (t) REVERT: A 1167 THR cc_start: 0.7686 (m) cc_final: 0.7182 (p) REVERT: A 1197 GLU cc_start: 0.7829 (tp30) cc_final: 0.7221 (tp30) REVERT: A 1273 ILE cc_start: 0.8078 (mt) cc_final: 0.7645 (mm) REVERT: A 1277 GLU cc_start: 0.7564 (tp30) cc_final: 0.6994 (tp30) REVERT: A 1287 LYS cc_start: 0.8287 (mmtm) cc_final: 0.8048 (mmtt) REVERT: A 1307 ASN cc_start: 0.8255 (p0) cc_final: 0.7521 (p0) REVERT: A 1309 LYS cc_start: 0.8287 (mmmt) cc_final: 0.7868 (mmmt) REVERT: A 1310 MET cc_start: 0.7840 (mmm) cc_final: 0.7632 (mmm) outliers start: 117 outliers final: 96 residues processed: 1017 average time/residue: 0.2503 time to fit residues: 405.4500 Evaluate side-chains 1061 residues out of total 4341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 951 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 457 ASN Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 392 ARG Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 471 GLN Chi-restraints excluded: chain G residue 513 PHE Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 547 TRP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 64 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 373 ASN Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 1043 ASN Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 350 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 283 optimal weight: 7.9990 chunk 392 optimal weight: 4.9990 chunk 277 optimal weight: 0.9980 chunk 399 optimal weight: 2.9990 chunk 418 optimal weight: 1.9990 chunk 370 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 chunk 274 optimal weight: 0.5980 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN D 457 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN G 177 ASN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN A 59 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.169357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.136559 restraints weight = 60569.839| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.02 r_work: 0.3654 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 39343 Z= 0.214 Angle : 0.705 10.400 53371 Z= 0.365 Chirality : 0.046 0.257 5851 Planarity : 0.005 0.060 6944 Dihedral : 6.795 96.153 5767 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.06 % Allowed : 22.07 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -1.00 (0.12), residues: 4890 helix: 0.17 (0.19), residues: 757 sheet: -0.33 (0.13), residues: 1460 loop : -1.08 (0.12), residues: 2673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 938 TYR 0.033 0.002 TYR D 141 PHE 0.031 0.002 PHE A1187 TRP 0.043 0.003 TRP E 416 HIS 0.012 0.001 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00469 (39230) covalent geometry : angle 0.69842 (53146) SS BOND : bond 0.00364 ( 93) SS BOND : angle 1.56579 ( 186) hydrogen bonds : bond 0.03964 ( 1212) hydrogen bonds : angle 5.47372 ( 3255) Misc. bond : bond 0.00054 ( 7) link_ALPHA1-2 : bond 0.00702 ( 1) link_ALPHA1-2 : angle 1.38894 ( 3) link_ALPHA1-3 : bond 0.00884 ( 1) link_ALPHA1-3 : angle 1.63936 ( 3) link_BETA1-4 : bond 0.00390 ( 5) link_BETA1-4 : angle 1.52929 ( 15) link_NAG-ASN : bond 0.00460 ( 6) link_NAG-ASN : angle 2.64303 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17965.85 seconds wall clock time: 305 minutes 34.15 seconds (18334.15 seconds total)