Starting phenix.real_space_refine on Fri Aug 7 02:04:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8or0_17114/08_2026/8or0_17114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8or0_17114/08_2026/8or0_17114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8or0_17114/08_2026/8or0_17114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8or0_17114/08_2026/8or0_17114.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8or0_17114/08_2026/8or0_17114.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8or0_17114/08_2026/8or0_17114.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8or0_17114/08_2026/8or0_17114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8or0_17114/08_2026/8or0_17114.map" } resolution = 3.1 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= 0.022 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 Zn 3 6.06 5 S 104 5.16 5 C 11921 2.51 5 N 3254 2.21 5 O 3541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18823 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5531 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 663} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 731 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 8847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1137, 8847 Classifications: {'peptide': 1137} Link IDs: {'PTRANS': 54, 'TRANS': 1082} Chain breaks: 6 Chain: "D" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain breaks: 3 Chain: "E" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 1899 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PTRANS': 13, 'TRANS': 293} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 563 Unresolved non-hydrogen angles: 726 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 10, 'PHE:plan': 8, 'GLN:plan1': 12, 'ARG:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 2, 'HIS:plan': 6, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 294 Chain: "G" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 319 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 5, 'ASP:plan': 4, 'GLU:plan': 7, 'PHE:plan': 2, 'ARG:plan': 4, 'HIS:plan': 5, 'TRP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 157 Chain: "H" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 421 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 7, 'TRANS': 77} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 4, 'TRP:plan': 4, 'TYR:plan': 5, 'ARG:plan': 6, 'ASP:plan': 5, 'PHE:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 173 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5756 SG CYS B 45 62.874 112.712 136.864 1.00 97.50 S ATOM 6051 SG CYS B 83 62.524 110.686 133.913 1.00 46.50 S ATOM 5980 SG CYS B 75 48.551 114.360 128.163 1.00 58.76 S ATOM 6147 SG CYS B 94 49.330 111.557 131.289 1.00 75.85 S ATOM 5823 SG CYS B 53 67.335 112.548 132.814 1.00109.50 S ATOM 5846 SG CYS B 56 69.792 110.689 130.542 1.00118.28 S ATOM 5930 SG CYS B 68 67.401 113.296 129.037 1.00 92.41 S Time building chain proxies: 4.49, per 1000 atoms: 0.24 Number of scatterers: 18823 At special positions: 0 Unit cell: (117.72, 177.12, 153.36, 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) Zn 3 29.99 S 104 16.00 O 3541 8.00 N 3254 7.00 C 11921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B4001 " pdb="ZN ZN B4001 " - pdb=" SG CYS B 45 " pdb="ZN ZN B4001 " - pdb=" ND1 HIS B 80 " pdb="ZN ZN B4001 " - pdb=" SG CYS B 83 " pdb=" ZN B4002 " pdb="ZN ZN B4002 " - pdb=" SG CYS B 75 " pdb="ZN ZN B4002 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B4002 " - pdb=" SG CYS B 94 " pdb=" ZN B4003 " pdb="ZN ZN B4003 " - pdb=" ND1 HIS B 82 " pdb="ZN ZN B4003 " - pdb=" SG CYS B 56 " pdb="ZN ZN B4003 " - pdb=" SG CYS B 53 " pdb="ZN ZN B4003 " - pdb=" SG CYS B 68 " Number of angles added : 3 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4798 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 8 sheets defined 65.2% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 18 through 33 removed outlier: 4.230A pdb=" N ASP A 22 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP A 23 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ALA A 26 " --> pdb=" O ASP A 22 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLY A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 52 removed outlier: 4.505A pdb=" N MET A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR A 50 " --> pdb=" O TYR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 106 removed outlier: 3.747A pdb=" N ASP A 106 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 137 Processing helix chain 'A' and resid 158 through 171 Processing helix chain 'A' and resid 174 through 192 removed outlier: 3.647A pdb=" N GLN A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 211 removed outlier: 4.196A pdb=" N VAL A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 231 through 255 Processing helix chain 'A' and resid 256 through 278 removed outlier: 3.767A pdb=" N LYS A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 298 removed outlier: 4.007A pdb=" N LYS A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 Processing helix chain 'A' and resid 315 through 327 removed outlier: 3.895A pdb=" N LEU A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 355 removed outlier: 3.841A pdb=" N CYS A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 384 removed outlier: 3.697A pdb=" N TYR A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 405 Processing helix chain 'A' and resid 406 through 413 removed outlier: 3.526A pdb=" N MET A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 431 Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.674A pdb=" N LYS A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 476 removed outlier: 3.819A pdb=" N PHE A 462 " --> pdb=" O ASP A 458 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 496 Processing helix chain 'A' and resid 497 through 525 removed outlier: 3.710A pdb=" N THR A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 504 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 574 removed outlier: 3.810A pdb=" N TYR A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 566 " --> pdb=" O SER A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 613 Processing helix chain 'A' and resid 621 through 630 removed outlier: 3.708A pdb=" N LEU A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 645 Processing helix chain 'A' and resid 690 through 719 removed outlier: 4.572A pdb=" N GLN A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 738 Processing helix chain 'A' and resid 745 through 759 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 53 through 59 removed outlier: 3.776A pdb=" N GLN B 57 " --> pdb=" O CYS B 53 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 80 through 88 Processing helix chain 'C' and resid 5 through 16 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 44 through 58 removed outlier: 3.807A pdb=" N GLU C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 79 removed outlier: 3.790A pdb=" N GLY C 73 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix removed outlier: 4.936A pdb=" N SER C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS C 78 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 96 removed outlier: 3.660A pdb=" N LEU C 96 " --> pdb=" O CYS C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 128 through 142 removed outlier: 3.903A pdb=" N LYS C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER C 140 " --> pdb=" O GLY C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 165 Processing helix chain 'C' and resid 172 through 181 Processing helix chain 'C' and resid 182 through 186 removed outlier: 3.580A pdb=" N THR C 185 " --> pdb=" O PRO C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 206 Processing helix chain 'C' and resid 213 through 227 removed outlier: 3.621A pdb=" N SER C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.930A pdb=" N ILE C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 265 Proline residue: C 258 - end of helix removed outlier: 3.954A pdb=" N ASN C 265 " --> pdb=" O VAL C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 4.381A pdb=" N TYR C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C 278 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE C 279 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C 280 " --> pdb=" O ILE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 302 removed outlier: 3.757A pdb=" N VAL C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 364 removed outlier: 3.635A pdb=" N VAL C 349 " --> pdb=" O MET C 345 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ARG C 351 " --> pdb=" O TRP C 347 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA C 353 " --> pdb=" O VAL C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 374 removed outlier: 3.635A pdb=" N THR C 374 " --> pdb=" O GLU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 383 Processing helix chain 'C' and resid 387 through 405 Processing helix chain 'C' and resid 423 through 443 removed outlier: 4.230A pdb=" N MET C 427 " --> pdb=" O THR C 423 " (cutoff:3.500A) Proline residue: C 433 - end of helix Processing helix chain 'C' and resid 447 through 465 removed outlier: 4.441A pdb=" N LEU C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 486 Proline residue: C 478 - end of helix Processing helix chain 'C' and resid 490 through 508 Processing helix chain 'C' and resid 509 through 513 Processing helix chain 'C' and resid 516 through 529 Proline residue: C 522 - end of helix removed outlier: 4.065A pdb=" N GLY C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 551 removed outlier: 3.621A pdb=" N THR C 536 " --> pdb=" O PHE C 532 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 551 " --> pdb=" O VAL C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 575 removed outlier: 3.509A pdb=" N ILE C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS C 566 " --> pdb=" O THR C 562 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP C 567 " --> pdb=" O PRO C 563 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N CYS C 571 " --> pdb=" O ASP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 601 Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.054A pdb=" N LEU C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 621 removed outlier: 4.127A pdb=" N LYS C 620 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN C 621 " --> pdb=" O GLU C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 Processing helix chain 'C' and resid 644 through 658 removed outlier: 3.718A pdb=" N GLY C 649 " --> pdb=" O ARG C 645 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU C 650 " --> pdb=" O PRO C 646 " (cutoff:3.500A) Proline residue: C 653 - end of helix removed outlier: 3.717A pdb=" N PHE C 658 " --> pdb=" O ILE C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 681 Processing helix chain 'C' and resid 686 through 696 removed outlier: 4.130A pdb=" N ILE C 690 " --> pdb=" O THR C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 723 removed outlier: 3.967A pdb=" N SER C 714 " --> pdb=" O GLN C 710 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE C 715 " --> pdb=" O MET C 711 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU C 716 " --> pdb=" O ALA C 712 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 721 " --> pdb=" O THR C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 749 through 765 Processing helix chain 'C' and resid 771 through 785 removed outlier: 3.639A pdb=" N LEU C 775 " --> pdb=" O GLY C 771 " (cutoff:3.500A) Proline residue: C 782 - end of helix Processing helix chain 'C' and resid 792 through 809 removed outlier: 3.673A pdb=" N TYR C 796 " --> pdb=" O HIS C 792 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA C 809 " --> pdb=" O ALA C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 826 Processing helix chain 'C' and resid 831 through 846 Processing helix chain 'C' and resid 857 through 866 Processing helix chain 'C' and resid 870 through 887 removed outlier: 4.300A pdb=" N SER C 874 " --> pdb=" O GLU C 870 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA C 875 " --> pdb=" O GLU C 871 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN C 887 " --> pdb=" O ILE C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 902 removed outlier: 3.770A pdb=" N TYR C 891 " --> pdb=" O ASN C 887 " (cutoff:3.500A) Proline residue: C 893 - end of helix Processing helix chain 'C' and resid 906 through 920 Processing helix chain 'C' and resid 921 through 926 Processing helix chain 'C' and resid 928 through 937 Processing helix chain 'C' and resid 938 through 941 removed outlier: 4.291A pdb=" N GLU C 941 " --> pdb=" O LYS C 938 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 938 through 941' Processing helix chain 'C' and resid 944 through 959 Processing helix chain 'C' and resid 962 through 971 Proline residue: C 968 - end of helix Processing helix chain 'C' and resid 972 through 977 removed outlier: 3.783A pdb=" N SER C 976 " --> pdb=" O GLY C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 990 Processing helix chain 'C' and resid 1000 through 1015 removed outlier: 3.680A pdb=" N ASN C1006 " --> pdb=" O PRO C1002 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLY C1009 " --> pdb=" O LYS C1005 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP C1010 " --> pdb=" O ASN C1006 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C1015 " --> pdb=" O PHE C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1037 Processing helix chain 'C' and resid 1038 through 1043 removed outlier: 3.735A pdb=" N ARG C1042 " --> pdb=" O SER C1039 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASP C1043 " --> pdb=" O LEU C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1044 through 1055 Proline residue: C1050 - end of helix removed outlier: 3.961A pdb=" N GLU C1055 " --> pdb=" O HIS C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1078 through 1096 Processing helix chain 'C' and resid 1101 through 1112 removed outlier: 3.957A pdb=" N PHE C1105 " --> pdb=" O ASP C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1133 Processing helix chain 'C' and resid 1134 through 1138 removed outlier: 4.045A pdb=" N ALA C1137 " --> pdb=" O CYS C1134 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1154 Proline residue: C1148 - end of helix Processing helix chain 'C' and resid 1163 through 1185 Processing helix chain 'C' and resid 1204 through 1210 Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 93 through 99 removed outlier: 4.175A pdb=" N GLU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 155 through 162 Processing helix chain 'E' and resid 101 through 110 removed outlier: 3.524A pdb=" N GLY E 107 " --> pdb=" O GLU E 103 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 120 Processing helix chain 'E' and resid 124 through 132 removed outlier: 4.042A pdb=" N SER E 132 " --> pdb=" O TYR E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 removed outlier: 3.887A pdb=" N THR E 152 " --> pdb=" O HIS E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 199 removed outlier: 3.523A pdb=" N LEU E 198 " --> pdb=" O VAL E 195 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS E 199 " --> pdb=" O SER E 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 195 through 199' Processing helix chain 'E' and resid 219 through 227 removed outlier: 3.828A pdb=" N VAL E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 255 removed outlier: 3.540A pdb=" N SER E 253 " --> pdb=" O GLN E 249 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS E 255 " --> pdb=" O LEU E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 274 Processing helix chain 'E' and resid 275 through 280 removed outlier: 3.967A pdb=" N ALA E 279 " --> pdb=" O GLN E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 309 removed outlier: 4.069A pdb=" N LEU E 302 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER E 303 " --> pdb=" O LYS E 299 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR E 304 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG E 307 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 4.404A pdb=" N PHE E 331 " --> pdb=" O CYS E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 356 removed outlier: 3.728A pdb=" N GLU E 355 " --> pdb=" O THR E 352 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 356 " --> pdb=" O LEU E 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 352 through 356' Processing helix chain 'E' and resid 377 through 383 removed outlier: 3.684A pdb=" N LYS E 380 " --> pdb=" O GLN E 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 31 removed outlier: 3.768A pdb=" N LYS G 30 " --> pdb=" O ASP G 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 175 Processing helix chain 'H' and resid 182 through 187 removed outlier: 3.921A pdb=" N ILE H 186 " --> pdb=" O THR H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 220 Processing sheet with id=AA1, first strand: chain 'A' and resid 537 through 541 Processing sheet with id=AA2, first strand: chain 'A' and resid 590 through 591 removed outlier: 3.682A pdb=" N GLU B 23 " --> pdb=" O VAL A 591 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 762 through 764 removed outlier: 3.509A pdb=" N GLU A 763 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.628A pdb=" N PHE D 14 " --> pdb=" O LEU D 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 185 through 187 removed outlier: 3.691A pdb=" N ASP E 187 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG E 164 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR E 139 " --> pdb=" O LEU E 416 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.553A pdb=" N MET E 170 " --> pdb=" O VAL E 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 213 through 214 removed outlier: 6.947A pdb=" N LEU E 213 " --> pdb=" O SER E 238 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 261 through 264 removed outlier: 3.779A pdb=" N LEU E 261 " --> pdb=" O GLN E 287 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN E 289 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 263 " --> pdb=" O ASN E 289 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER E 291 " --> pdb=" O LEU E 263 " (cutoff:3.500A) 1014 hydrogen bonds defined for protein. 3012 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: 3.39 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3204 1.31 - 1.43: 4547 1.43 - 1.56: 11190 1.56 - 1.69: 3 1.69 - 1.82: 152 Bond restraints: 19096 Sorted by residual: bond pdb=" N LYS C1156 " pdb=" CA LYS C1156 " ideal model delta sigma weight residual 1.456 1.376 0.080 1.21e-02 6.83e+03 4.39e+01 bond pdb=" N THR C1154 " pdb=" CA THR C1154 " ideal model delta sigma weight residual 1.463 1.382 0.081 1.31e-02 5.83e+03 3.81e+01 bond pdb=" CA THR C1155 " pdb=" C THR C1155 " ideal model delta sigma weight residual 1.521 1.452 0.069 1.19e-02 7.06e+03 3.35e+01 bond pdb=" CA VAL C1157 " pdb=" C VAL C1157 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.14e-02 7.69e+03 3.12e+01 bond pdb=" CA VAL C1162 " pdb=" CB VAL C1162 " ideal model delta sigma weight residual 1.538 1.486 0.053 9.80e-03 1.04e+04 2.89e+01 ... (remaining 19091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 25698 3.23 - 6.47: 136 6.47 - 9.70: 17 9.70 - 12.94: 5 12.94 - 16.17: 2 Bond angle restraints: 25858 Sorted by residual: angle pdb=" CA PRO C1206 " pdb=" N PRO C1206 " pdb=" CD PRO C1206 " ideal model delta sigma weight residual 112.00 95.83 16.17 1.40e+00 5.10e-01 1.33e+02 angle pdb=" N LYS C1163 " pdb=" CA LYS C1163 " pdb=" C LYS C1163 " ideal model delta sigma weight residual 112.34 122.20 -9.86 1.30e+00 5.92e-01 5.75e+01 angle pdb=" C GLU C1171 " pdb=" N LEU C1172 " pdb=" CA LEU C1172 " ideal model delta sigma weight residual 120.58 107.75 12.83 1.71e+00 3.42e-01 5.63e+01 angle pdb=" N PRO C1206 " pdb=" CD PRO C1206 " pdb=" CG PRO C1206 " ideal model delta sigma weight residual 103.20 93.91 9.29 1.50e+00 4.44e-01 3.83e+01 angle pdb=" N THR C1154 " pdb=" CA THR C1154 " pdb=" C THR C1154 " ideal model delta sigma weight residual 111.81 103.01 8.80 1.44e+00 4.82e-01 3.74e+01 ... (remaining 25853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 10275 17.63 - 35.27: 1134 35.27 - 52.90: 256 52.90 - 70.53: 40 70.53 - 88.17: 20 Dihedral angle restraints: 11725 sinusoidal: 4404 harmonic: 7321 Sorted by residual: dihedral pdb=" N ASN C1160 " pdb=" C ASN C1160 " pdb=" CA ASN C1160 " pdb=" CB ASN C1160 " ideal model delta harmonic sigma weight residual 122.80 135.69 -12.89 0 2.50e+00 1.60e-01 2.66e+01 dihedral pdb=" CA LEU E 188 " pdb=" C LEU E 188 " pdb=" N SER E 189 " pdb=" CA SER E 189 " ideal model delta harmonic sigma weight residual 180.00 156.73 23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA SER A 231 " pdb=" C SER A 231 " pdb=" N PHE A 232 " pdb=" CA PHE A 232 " ideal model delta harmonic sigma weight residual -180.00 -158.68 -21.32 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 11722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2881 0.075 - 0.150: 195 0.150 - 0.225: 7 0.225 - 0.300: 2 0.300 - 0.375: 3 Chirality restraints: 3088 Sorted by residual: chirality pdb=" CA ASN C1160 " pdb=" N ASN C1160 " pdb=" C ASN C1160 " pdb=" CB ASN C1160 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA LYS C1163 " pdb=" N LYS C1163 " pdb=" C LYS C1163 " pdb=" CB LYS C1163 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CG LEU E 156 " pdb=" CB LEU E 156 " pdb=" CD1 LEU E 156 " pdb=" CD2 LEU E 156 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 3085 not shown) Planarity restraints: 3294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C1153 " 0.036 2.00e-02 2.50e+03 7.59e-02 5.76e+01 pdb=" C CYS C1153 " -0.131 2.00e-02 2.50e+03 pdb=" O CYS C1153 " 0.050 2.00e-02 2.50e+03 pdb=" N THR C1154 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C1205 " 0.101 5.00e-02 4.00e+02 1.39e-01 3.11e+01 pdb=" N PRO C1206 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO C1206 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO C1206 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C1162 " 0.024 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C VAL C1162 " -0.084 2.00e-02 2.50e+03 pdb=" O VAL C1162 " 0.032 2.00e-02 2.50e+03 pdb=" N LYS C1163 " 0.028 2.00e-02 2.50e+03 ... (remaining 3291 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 5 1.90 - 2.65: 214 2.65 - 3.40: 26769 3.40 - 4.15: 39574 4.15 - 4.90: 72541 Nonbonded interactions: 139103 Sorted by model distance: nonbonded pdb=" OD2 ASP C1170 " pdb=" NH2 ARG C1174 " model vdw 1.149 3.120 nonbonded pdb=" OD1 ASP C1170 " pdb=" NH1 ARG C1174 " model vdw 1.527 3.120 nonbonded pdb=" OD2 ASP C1170 " pdb=" CZ ARG C1174 " model vdw 1.722 3.270 nonbonded pdb=" OD1 ASP C1170 " pdb=" CZ ARG C1174 " model vdw 1.797 3.270 nonbonded pdb=" CG ASP C1170 " pdb=" NH1 ARG C1174 " model vdw 1.820 3.350 ... (remaining 139098 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.310 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5613 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 : 0.004 0.187 19106 Z= 0.224 Angle : 0.638 16.173 25861 Z= 0.347 Chirality : 0.040 0.375 3088 Planarity : 0.005 0.139 3294 Dihedral : 15.612 88.167 6927 Min Nonbonded Distance : 1.149 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.51 % Allowed : 14.37 % Favored : 85.12 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.18), residues: 2429 helix: 1.84 (0.14), residues: 1431 sheet: -2.06 (0.90), residues: 33 loop : -1.86 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 382 TYR 0.016 0.001 TYR C 291 PHE 0.026 0.001 PHE A 402 TRP 0.021 0.001 TRP A 545 HIS 0.012 0.001 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.22 (19096) covalent geometry : angle 0.63815 / 0.35 (25858) hydrogen bonds : bond 0.12789 / 8.55 ( 1014) hydrogen bonds : angle 4.70249 / 3.33 ( 3012) metal coordination : bond 0.00720 / 0.47 ( 10) metal coordination : angle 0.43620 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 282 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6590 (mp0) REVERT: A 323 TYR cc_start: 0.7721 (t80) cc_final: 0.7436 (t80) REVERT: C 463 ASN cc_start: 0.7483 (t0) cc_final: 0.7263 (t0) REVERT: C 654 ILE cc_start: 0.7116 (mm) cc_final: 0.6752 (tp) REVERT: C 1068 MET cc_start: 0.1726 (mtt) cc_final: 0.1296 (tpt) REVERT: C 1169 GLN cc_start: 0.7295 (mm110) cc_final: 0.6956 (mt0) outliers start: 10 outliers final: 8 residues processed: 285 average time/residue: 0.1491 time to fit residues: 65.8496 Evaluate side-chains 278 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 270 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 994 SER Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1165 GLU Chi-restraints excluded: chain C residue 1168 LYS Chi-restraints excluded: chain C residue 1170 ASP Chi-restraints excluded: chain C residue 1171 GLU Chi-restraints excluded: chain E residue 133 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.0770 chunk 194 optimal weight: 0.0970 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0670 chunk 235 optimal weight: 6.9990 overall best weight: 0.2232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS B 92 GLN C 365 HIS C 452 GLN C 514 HIS C 911 HIS C1140 GLN C1169 GLN D 23 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.222872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.200723 restraints weight = 31583.269| |-----------------------------------------------------------------------------| r_work (start): 0.4650 rms_B_bonded: 3.05 r_work: 0.4551 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5731 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 19106 Z= 0.108 Angle : 0.523 9.479 25861 Z= 0.264 Chirality : 0.038 0.144 3088 Planarity : 0.004 0.059 3294 Dihedral : 4.674 128.407 2642 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.95 % Allowed : 12.42 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.18), residues: 2429 helix: 1.93 (0.14), residues: 1446 sheet: -2.42 (1.06), residues: 22 loop : -1.74 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1174 TYR 0.014 0.001 TYR C 291 PHE 0.024 0.001 PHE A 402 TRP 0.016 0.001 TRP C 933 HIS 0.009 0.001 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (19096) covalent geometry : angle 0.52304 / 0.26 (25858) hydrogen bonds : bond 0.02900 / 1.91 ( 1014) hydrogen bonds : angle 3.79302 / 2.67 ( 3012) metal coordination : bond 0.00744 / 0.49 ( 10) metal coordination : angle 0.66036 / 0.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 288 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLU cc_start: 0.6238 (mm-30) cc_final: 0.5990 (mm-30) REVERT: A 323 TYR cc_start: 0.7543 (t80) cc_final: 0.7292 (t80) REVERT: A 705 GLU cc_start: 0.6842 (mp0) cc_final: 0.6611 (mp0) REVERT: C 443 MET cc_start: 0.4358 (mmt) cc_final: 0.3771 (mmt) REVERT: C 654 ILE cc_start: 0.6977 (mm) cc_final: 0.6634 (tp) REVERT: C 1068 MET cc_start: 0.1917 (mtt) cc_final: 0.1367 (tpt) REVERT: C 1177 MET cc_start: 0.6558 (mmp) cc_final: 0.6265 (mmm) REVERT: E 235 LEU cc_start: 0.3898 (OUTLIER) cc_final: 0.3616 (tt) outliers start: 38 outliers final: 15 residues processed: 309 average time/residue: 0.1423 time to fit residues: 68.2440 Evaluate side-chains 301 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 285 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 1044 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 236 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.0148 > 50:) chunk 212 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 148 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 GLN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN A 696 GLN C 452 GLN C 854 GLN C 911 HIS C1036 ASN C1160 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.204007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.178886 restraints weight = 29647.692| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 2.95 r_work: 0.4320 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19106 Z= 0.172 Angle : 0.664 10.135 25861 Z= 0.335 Chirality : 0.043 0.320 3088 Planarity : 0.005 0.059 3294 Dihedral : 3.913 44.030 2625 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.08 % Allowed : 13.75 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.17), residues: 2429 helix: 1.36 (0.14), residues: 1433 sheet: -2.39 (1.04), residues: 22 loop : -1.75 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 948 TYR 0.025 0.002 TYR A 244 PHE 0.022 0.003 PHE A 402 TRP 0.034 0.003 TRP B 101 HIS 0.019 0.002 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (19096) covalent geometry : angle 0.66393 / 0.34 (25858) hydrogen bonds : bond 0.04395 / 2.84 ( 1014) hydrogen bonds : angle 4.17477 / 2.92 ( 3012) metal coordination : bond 0.01120 / 0.70 ( 10) metal coordination : angle 0.90224 / 0.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 329 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.7061 (mp0) cc_final: 0.6782 (mp0) REVERT: A 411 MET cc_start: 0.4417 (ppp) cc_final: 0.4074 (ppp) REVERT: A 589 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5727 (mp0) REVERT: A 706 ASP cc_start: 0.7008 (m-30) cc_final: 0.6759 (m-30) REVERT: C 58 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6879 (mm-30) REVERT: C 83 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: C 116 GLU cc_start: 0.6502 (mp0) cc_final: 0.6268 (tp30) REVERT: C 158 MET cc_start: 0.5611 (mmm) cc_final: 0.5292 (tpt) REVERT: C 231 THR cc_start: 0.1476 (OUTLIER) cc_final: 0.1177 (m) REVERT: C 446 LYS cc_start: 0.7701 (mmpt) cc_final: 0.7466 (mmpt) REVERT: C 517 VAL cc_start: 0.6449 (m) cc_final: 0.6035 (t) REVERT: C 897 GLN cc_start: 0.7515 (mm-40) cc_final: 0.7160 (mm-40) REVERT: C 905 ARG cc_start: 0.5242 (ttt-90) cc_final: 0.4712 (ttt90) REVERT: C 1118 ASP cc_start: 0.5609 (p0) cc_final: 0.5358 (p0) REVERT: C 1125 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7782 (tt) REVERT: C 1170 ASP cc_start: 0.7849 (t70) cc_final: 0.7615 (t0) REVERT: C 1171 GLU cc_start: 0.7289 (tp30) cc_final: 0.7023 (tp30) REVERT: C 1177 MET cc_start: 0.7436 (mmp) cc_final: 0.7135 (mmm) REVERT: C 1178 ARG cc_start: 0.7059 (ttm170) cc_final: 0.6711 (mtt180) REVERT: C 1197 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.5634 (mt-10) REVERT: D 165 TRP cc_start: 0.5668 (p-90) cc_final: 0.5227 (p-90) REVERT: E 123 VAL cc_start: 0.7612 (m) cc_final: 0.7372 (m) REVERT: E 133 ASP cc_start: 0.6695 (m-30) cc_final: 0.6427 (m-30) outliers start: 60 outliers final: 31 residues processed: 359 average time/residue: 0.1260 time to fit residues: 69.5581 Evaluate side-chains 334 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 298 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 449 LYS Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1044 LEU Chi-restraints excluded: chain C residue 1080 ASP Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1197 GLU Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 156 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 12 optimal weight: 0.0870 chunk 65 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 3 optimal weight: 0.4980 chunk 1 optimal weight: 0.0070 chunk 152 optimal weight: 0.0670 chunk 208 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 0.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 911 HIS ** C1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.204917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.179352 restraints weight = 30281.244| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 3.07 r_work: 0.4339 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19106 Z= 0.113 Angle : 0.559 8.883 25861 Z= 0.281 Chirality : 0.039 0.294 3088 Planarity : 0.004 0.050 3294 Dihedral : 3.596 44.858 2625 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.41 % Allowed : 16.11 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.17), residues: 2429 helix: 1.58 (0.14), residues: 1432 sheet: -2.23 (1.07), residues: 22 loop : -1.69 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 473 TYR 0.022 0.002 TYR A 244 PHE 0.032 0.002 PHE A 498 TRP 0.025 0.001 TRP D 94 HIS 0.013 0.001 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (19096) covalent geometry : angle 0.55856 / 0.28 (25858) hydrogen bonds : bond 0.03081 / 2.00 ( 1014) hydrogen bonds : angle 3.91696 / 2.73 ( 3012) metal coordination : bond 0.00758 / 0.49 ( 10) metal coordination : angle 0.76691 / 0.39 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 325 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 TYR cc_start: 0.6515 (m-80) cc_final: 0.5852 (m-80) REVERT: A 250 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6603 (mp0) REVERT: A 688 MET cc_start: 0.5053 (OUTLIER) cc_final: 0.4713 (tpp) REVERT: A 705 GLU cc_start: 0.6864 (mp0) cc_final: 0.6632 (mp0) REVERT: C 58 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6683 (mm-30) REVERT: C 181 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6819 (mp) REVERT: C 254 GLU cc_start: 0.6636 (mp0) cc_final: 0.6329 (mp0) REVERT: C 446 LYS cc_start: 0.7594 (mmpt) cc_final: 0.7356 (mmpt) REVERT: C 517 VAL cc_start: 0.6268 (m) cc_final: 0.5883 (t) REVERT: C 706 MET cc_start: 0.6648 (mmm) cc_final: 0.6223 (mmm) REVERT: C 839 LEU cc_start: 0.6563 (mt) cc_final: 0.6243 (mt) REVERT: C 897 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7293 (mm-40) REVERT: C 905 ARG cc_start: 0.5391 (ttt-90) cc_final: 0.4564 (ttt90) REVERT: C 911 HIS cc_start: 0.7639 (OUTLIER) cc_final: 0.7337 (m90) REVERT: C 964 GLU cc_start: 0.6286 (mp0) cc_final: 0.5954 (mp0) REVERT: C 1125 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7740 (tt) REVERT: C 1170 ASP cc_start: 0.7850 (t70) cc_final: 0.7631 (t0) REVERT: C 1177 MET cc_start: 0.7454 (mmp) cc_final: 0.7153 (mmm) REVERT: C 1197 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.5226 (mt-10) REVERT: D 165 TRP cc_start: 0.5447 (p-90) cc_final: 0.4952 (p-90) REVERT: E 123 VAL cc_start: 0.7673 (m) cc_final: 0.7443 (m) REVERT: E 133 ASP cc_start: 0.6692 (m-30) cc_final: 0.6418 (m-30) REVERT: E 217 ARG cc_start: 0.6628 (mmm160) cc_final: 0.6146 (tpm170) REVERT: E 235 LEU cc_start: 0.4543 (OUTLIER) cc_final: 0.4212 (tt) outliers start: 47 outliers final: 26 residues processed: 349 average time/residue: 0.1261 time to fit residues: 67.9163 Evaluate side-chains 341 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 308 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 449 LYS Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 911 HIS Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1044 LEU Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1197 GLU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 127 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 223 optimal weight: 0.5980 chunk 205 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 225 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 GLN A 737 GLN C 442 GLN C 748 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.198515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.172943 restraints weight = 29263.942| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 3.00 r_work: 0.4256 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19106 Z= 0.157 Angle : 0.601 8.919 25861 Z= 0.303 Chirality : 0.041 0.294 3088 Planarity : 0.004 0.048 3294 Dihedral : 3.736 41.593 2625 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.98 % Allowed : 16.68 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2429 helix: 1.35 (0.14), residues: 1443 sheet: -2.19 (1.04), residues: 22 loop : -1.64 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 969 TYR 0.019 0.002 TYR A 126 PHE 0.035 0.002 PHE A 498 TRP 0.022 0.002 TRP D 94 HIS 0.060 0.002 HIS C 911 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (19096) covalent geometry : angle 0.60075 / 0.30 (25858) hydrogen bonds : bond 0.03710 / 2.41 ( 1014) hydrogen bonds : angle 4.05500 / 2.83 ( 3012) metal coordination : bond 0.01008 / 0.65 ( 10) metal coordination : angle 0.60636 / 0.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 310 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.7185 (t80) cc_final: 0.6742 (t80) REVERT: A 250 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6680 (mm-30) REVERT: A 259 GLU cc_start: 0.7420 (tp30) cc_final: 0.7101 (tp30) REVERT: A 338 LYS cc_start: 0.7895 (tptp) cc_final: 0.7654 (tptp) REVERT: A 411 MET cc_start: 0.5243 (ppp) cc_final: 0.4833 (ptp) REVERT: A 633 MET cc_start: 0.5773 (tpp) cc_final: 0.5425 (tpp) REVERT: A 774 TYR cc_start: 0.5270 (t80) cc_final: 0.4500 (t80) REVERT: C 116 GLU cc_start: 0.6638 (tp30) cc_final: 0.6420 (tp30) REVERT: C 231 THR cc_start: 0.1742 (OUTLIER) cc_final: 0.1279 (p) REVERT: C 254 GLU cc_start: 0.6754 (mp0) cc_final: 0.6453 (mp0) REVERT: C 446 LYS cc_start: 0.7675 (mmpt) cc_final: 0.7433 (mmpt) REVERT: C 517 VAL cc_start: 0.6359 (m) cc_final: 0.6038 (t) REVERT: C 706 MET cc_start: 0.6952 (mmm) cc_final: 0.6556 (mmm) REVERT: C 820 GLN cc_start: 0.6651 (OUTLIER) cc_final: 0.5528 (tt0) REVERT: C 897 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7380 (mm-40) REVERT: C 905 ARG cc_start: 0.5908 (ttt-90) cc_final: 0.5259 (ttt90) REVERT: C 915 GLU cc_start: 0.6363 (tp30) cc_final: 0.6152 (tp30) REVERT: C 945 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7371 (tm-30) REVERT: C 1125 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7824 (tt) REVERT: C 1171 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7162 (tp30) REVERT: C 1197 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.5981 (mt-10) REVERT: D 4 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7357 (mp) REVERT: D 165 TRP cc_start: 0.5729 (p-90) cc_final: 0.5122 (p-90) REVERT: E 123 VAL cc_start: 0.7699 (m) cc_final: 0.7466 (m) REVERT: E 133 ASP cc_start: 0.6838 (m-30) cc_final: 0.6557 (m-30) REVERT: E 147 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5634 (mm) REVERT: E 216 LEU cc_start: 0.6769 (tp) cc_final: 0.6469 (mp) REVERT: E 235 LEU cc_start: 0.4844 (OUTLIER) cc_final: 0.4511 (tt) outliers start: 58 outliers final: 36 residues processed: 339 average time/residue: 0.1205 time to fit residues: 62.5340 Evaluate side-chains 343 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 298 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 711 MET Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 755 MET Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 820 GLN Chi-restraints excluded: chain C residue 931 ASN Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1044 LEU Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1131 SER Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1171 GLU Chi-restraints excluded: chain C residue 1197 GLU Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 187 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 126 optimal weight: 0.0770 chunk 244 optimal weight: 10.0000 chunk 142 optimal weight: 0.0000 chunk 113 optimal weight: 0.5980 overall best weight: 0.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 GLN A 276 GLN C 442 GLN C 911 HIS D 49 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.197901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.172503 restraints weight = 28992.575| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 2.94 r_work: 0.4251 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19106 Z= 0.123 Angle : 0.582 10.565 25861 Z= 0.289 Chirality : 0.040 0.287 3088 Planarity : 0.004 0.045 3294 Dihedral : 3.669 40.797 2625 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.03 % Allowed : 17.50 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.17), residues: 2429 helix: 1.38 (0.14), residues: 1442 sheet: -1.94 (1.08), residues: 22 loop : -1.63 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 382 TYR 0.017 0.002 TYR A 244 PHE 0.037 0.002 PHE A 498 TRP 0.022 0.002 TRP D 94 HIS 0.011 0.001 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (19096) covalent geometry : angle 0.58219 / 0.29 (25858) hydrogen bonds : bond 0.03339 / 2.17 ( 1014) hydrogen bonds : angle 4.04512 / 2.82 ( 3012) metal coordination : bond 0.00923 / 0.59 ( 10) metal coordination : angle 0.68325 / 0.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 309 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.7237 (mpp) cc_final: 0.6959 (mpp) REVERT: A 139 TYR cc_start: 0.7113 (t80) cc_final: 0.6737 (t80) REVERT: A 235 GLN cc_start: 0.7029 (pt0) cc_final: 0.6732 (pt0) REVERT: A 250 GLU cc_start: 0.6909 (mp0) cc_final: 0.6673 (mm-30) REVERT: A 335 GLU cc_start: 0.7071 (tp30) cc_final: 0.6643 (tp30) REVERT: A 338 LYS cc_start: 0.7849 (tptp) cc_final: 0.7618 (tptp) REVERT: A 411 MET cc_start: 0.5661 (ppp) cc_final: 0.5359 (ptp) REVERT: A 712 GLN cc_start: 0.6134 (tt0) cc_final: 0.5899 (tt0) REVERT: A 774 TYR cc_start: 0.5259 (t80) cc_final: 0.4463 (t80) REVERT: C 116 GLU cc_start: 0.6664 (tp30) cc_final: 0.6459 (tp30) REVERT: C 254 GLU cc_start: 0.6520 (mp0) cc_final: 0.6061 (mp0) REVERT: C 517 VAL cc_start: 0.6208 (m) cc_final: 0.5901 (t) REVERT: C 650 GLU cc_start: 0.6092 (tm-30) cc_final: 0.5718 (tm-30) REVERT: C 706 MET cc_start: 0.6938 (mmm) cc_final: 0.6501 (mmt) REVERT: C 820 GLN cc_start: 0.6636 (OUTLIER) cc_final: 0.5672 (tt0) REVERT: C 897 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7383 (mm-40) REVERT: C 905 ARG cc_start: 0.6336 (ttt-90) cc_final: 0.5614 (ttt90) REVERT: C 911 HIS cc_start: 0.7562 (OUTLIER) cc_final: 0.7188 (m90) REVERT: C 945 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7407 (tm-30) REVERT: C 947 THR cc_start: 0.7488 (m) cc_final: 0.7263 (p) REVERT: C 1125 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7933 (tt) REVERT: C 1142 LEU cc_start: 0.7222 (mt) cc_final: 0.7017 (mp) REVERT: C 1197 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.5827 (mt-10) REVERT: E 123 VAL cc_start: 0.7726 (m) cc_final: 0.7499 (m) REVERT: E 133 ASP cc_start: 0.6705 (m-30) cc_final: 0.6442 (m-30) REVERT: E 235 LEU cc_start: 0.4967 (OUTLIER) cc_final: 0.4631 (tt) outliers start: 59 outliers final: 34 residues processed: 340 average time/residue: 0.1315 time to fit residues: 68.3246 Evaluate side-chains 335 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 296 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 711 MET Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 820 GLN Chi-restraints excluded: chain C residue 911 HIS Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1044 LEU Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1131 SER Chi-restraints excluded: chain C residue 1197 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 212 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 148 optimal weight: 0.4980 chunk 242 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN A 615 ASN C 440 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.195031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.169086 restraints weight = 29150.103| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 2.99 r_work: 0.4219 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19106 Z= 0.141 Angle : 0.622 13.338 25861 Z= 0.307 Chirality : 0.041 0.277 3088 Planarity : 0.004 0.045 3294 Dihedral : 3.669 22.053 2624 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.98 % Allowed : 18.62 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.17), residues: 2429 helix: 1.30 (0.14), residues: 1440 sheet: -1.88 (1.09), residues: 22 loop : -1.61 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 191 TYR 0.023 0.002 TYR A 244 PHE 0.038 0.002 PHE C 282 TRP 0.024 0.002 TRP C 933 HIS 0.012 0.001 HIS C 911 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (19096) covalent geometry : angle 0.62167 / 0.31 (25858) hydrogen bonds : bond 0.03710 / 2.40 ( 1014) hydrogen bonds : angle 4.13114 / 2.87 ( 3012) metal coordination : bond 0.00945 / 0.60 ( 10) metal coordination : angle 0.58968 / 0.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 304 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.7183 (mpp) cc_final: 0.6924 (mpp) REVERT: A 250 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6725 (mm-30) REVERT: A 259 GLU cc_start: 0.7607 (tp30) cc_final: 0.7204 (tp30) REVERT: A 335 GLU cc_start: 0.7272 (tp30) cc_final: 0.6842 (tp30) REVERT: A 338 LYS cc_start: 0.7870 (tptp) cc_final: 0.7662 (tptp) REVERT: A 411 MET cc_start: 0.5981 (ppp) cc_final: 0.5779 (ptp) REVERT: A 712 GLN cc_start: 0.6145 (tt0) cc_final: 0.5908 (tt0) REVERT: A 774 TYR cc_start: 0.5422 (t80) cc_final: 0.4585 (t80) REVERT: C 116 GLU cc_start: 0.6756 (tp30) cc_final: 0.6530 (tp30) REVERT: C 231 THR cc_start: 0.1730 (OUTLIER) cc_final: 0.1270 (p) REVERT: C 403 LYS cc_start: 0.7916 (mttp) cc_final: 0.7671 (mttp) REVERT: C 406 ARG cc_start: 0.7412 (mpt-90) cc_final: 0.7036 (mtt90) REVERT: C 517 VAL cc_start: 0.6025 (m) cc_final: 0.5766 (t) REVERT: C 820 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.5890 (tt0) REVERT: C 897 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7587 (mm-40) REVERT: C 911 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.7444 (m-70) REVERT: C 945 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7459 (tm-30) REVERT: C 947 THR cc_start: 0.7522 (m) cc_final: 0.7281 (p) REVERT: C 1125 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7934 (tt) REVERT: C 1197 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.5953 (mt-10) REVERT: E 123 VAL cc_start: 0.7729 (m) cc_final: 0.7499 (m) REVERT: E 133 ASP cc_start: 0.6782 (m-30) cc_final: 0.6493 (m-30) REVERT: E 235 LEU cc_start: 0.5133 (OUTLIER) cc_final: 0.4802 (tt) outliers start: 58 outliers final: 35 residues processed: 336 average time/residue: 0.1447 time to fit residues: 74.9556 Evaluate side-chains 338 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 296 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 711 MET Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 820 GLN Chi-restraints excluded: chain C residue 911 HIS Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1044 LEU Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1131 SER Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1197 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 117 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 90 optimal weight: 0.0970 chunk 205 optimal weight: 0.4980 chunk 72 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 215 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.193539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.167907 restraints weight = 28760.383| |-----------------------------------------------------------------------------| r_work (start): 0.4331 rms_B_bonded: 2.97 r_work: 0.4209 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19106 Z= 0.138 Angle : 0.635 10.778 25861 Z= 0.317 Chirality : 0.041 0.281 3088 Planarity : 0.004 0.050 3294 Dihedral : 3.725 21.533 2624 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.77 % Allowed : 18.88 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2429 helix: 1.25 (0.14), residues: 1442 sheet: -1.87 (1.09), residues: 22 loop : -1.64 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 191 TYR 0.024 0.002 TYR A 244 PHE 0.033 0.002 PHE A 535 TRP 0.021 0.002 TRP C 933 HIS 0.030 0.001 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (19096) covalent geometry : angle 0.63456 / 0.32 (25858) hydrogen bonds : bond 0.03649 / 2.37 ( 1014) hydrogen bonds : angle 4.17028 / 2.90 ( 3012) metal coordination : bond 0.00979 / 0.61 ( 10) metal coordination : angle 0.60578 / 0.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 305 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.7190 (mpp) cc_final: 0.6900 (mpp) REVERT: A 139 TYR cc_start: 0.7250 (t80) cc_final: 0.6815 (t80) REVERT: A 250 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6630 (mm-30) REVERT: A 335 GLU cc_start: 0.7435 (tp30) cc_final: 0.6979 (tp30) REVERT: A 338 LYS cc_start: 0.7885 (tptp) cc_final: 0.7677 (tptp) REVERT: A 774 TYR cc_start: 0.5381 (t80) cc_final: 0.4517 (t80) REVERT: C 116 GLU cc_start: 0.6799 (tp30) cc_final: 0.6532 (tp30) REVERT: C 137 ARG cc_start: 0.6880 (ttm-80) cc_final: 0.6607 (mmm-85) REVERT: C 272 ARG cc_start: 0.4986 (mpp80) cc_final: 0.4618 (ttp80) REVERT: C 403 LYS cc_start: 0.7964 (mttp) cc_final: 0.7698 (mttp) REVERT: C 406 ARG cc_start: 0.7409 (mpt-90) cc_final: 0.7050 (mtt90) REVERT: C 517 VAL cc_start: 0.5947 (m) cc_final: 0.5708 (t) REVERT: C 820 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.5965 (tt0) REVERT: C 847 HIS cc_start: 0.5770 (OUTLIER) cc_final: 0.4730 (t70) REVERT: C 850 ASP cc_start: 0.7470 (t0) cc_final: 0.7244 (t0) REVERT: C 897 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7617 (mm-40) REVERT: C 1068 MET cc_start: 0.3343 (tpt) cc_final: 0.2932 (tpt) REVERT: C 1125 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7907 (tt) REVERT: C 1178 ARG cc_start: 0.7175 (ttm170) cc_final: 0.6764 (mtt-85) REVERT: C 1197 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.5406 (mt-10) REVERT: D 7 GLN cc_start: 0.6158 (tp40) cc_final: 0.5826 (tp40) REVERT: E 123 VAL cc_start: 0.7736 (m) cc_final: 0.7498 (m) REVERT: E 130 LEU cc_start: 0.7526 (mm) cc_final: 0.7265 (mm) REVERT: E 133 ASP cc_start: 0.6789 (m-30) cc_final: 0.6450 (m-30) REVERT: E 147 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6341 (mm) REVERT: E 235 LEU cc_start: 0.5243 (OUTLIER) cc_final: 0.4904 (tt) outliers start: 54 outliers final: 33 residues processed: 335 average time/residue: 0.1419 time to fit residues: 73.1673 Evaluate side-chains 334 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 294 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 711 MET Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 820 GLN Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1131 SER Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1197 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 167 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 46 optimal weight: 0.1980 chunk 156 optimal weight: 0.0000 chunk 229 optimal weight: 0.0020 chunk 161 optimal weight: 0.0170 overall best weight: 0.0628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 GLN A 255 ASN C 442 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.197101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.171738 restraints weight = 28940.087| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 2.98 r_work: 0.4245 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19106 Z= 0.117 Angle : 0.615 13.047 25861 Z= 0.305 Chirality : 0.040 0.250 3088 Planarity : 0.004 0.043 3294 Dihedral : 3.553 20.351 2624 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.21 % Allowed : 19.81 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.17), residues: 2429 helix: 1.39 (0.14), residues: 1442 sheet: -1.89 (1.11), residues: 22 loop : -1.57 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 191 TYR 0.032 0.001 TYR C1117 PHE 0.033 0.002 PHE C 282 TRP 0.017 0.001 TRP D 94 HIS 0.020 0.001 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (19096) covalent geometry : angle 0.61466 / 0.30 (25858) hydrogen bonds : bond 0.03155 / 2.05 ( 1014) hydrogen bonds : angle 4.06738 / 2.84 ( 3012) metal coordination : bond 0.00703 / 0.43 ( 10) metal coordination : angle 0.55007 / 0.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 302 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.7155 (mpp) cc_final: 0.6868 (mpp) REVERT: A 335 GLU cc_start: 0.7388 (tp30) cc_final: 0.6937 (tp30) REVERT: A 338 LYS cc_start: 0.7888 (tptp) cc_final: 0.7676 (tptp) REVERT: A 507 MET cc_start: 0.4104 (mtm) cc_final: 0.3411 (mtm) REVERT: A 774 TYR cc_start: 0.5257 (t80) cc_final: 0.4467 (t80) REVERT: C 25 MET cc_start: 0.6120 (mmt) cc_final: 0.5651 (tpp) REVERT: C 116 GLU cc_start: 0.6725 (tp30) cc_final: 0.6486 (tp30) REVERT: C 137 ARG cc_start: 0.6875 (ttm-80) cc_final: 0.6626 (mmm-85) REVERT: C 272 ARG cc_start: 0.4880 (mpp80) cc_final: 0.4629 (ttp80) REVERT: C 403 LYS cc_start: 0.7887 (mttp) cc_final: 0.7659 (mttp) REVERT: C 517 VAL cc_start: 0.5952 (m) cc_final: 0.5694 (t) REVERT: C 820 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6236 (mt0) REVERT: C 897 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7631 (mm-40) REVERT: C 1125 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7896 (tt) REVERT: C 1197 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.5788 (mt-10) REVERT: D 7 GLN cc_start: 0.6085 (tp40) cc_final: 0.5756 (tp40) REVERT: E 123 VAL cc_start: 0.7654 (m) cc_final: 0.7431 (m) REVERT: E 130 LEU cc_start: 0.7392 (mm) cc_final: 0.7188 (mm) REVERT: E 133 ASP cc_start: 0.6778 (m-30) cc_final: 0.6444 (m-30) REVERT: E 145 LYS cc_start: 0.7655 (mmtt) cc_final: 0.7449 (mptt) REVERT: E 147 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6359 (mm) REVERT: E 235 LEU cc_start: 0.5149 (OUTLIER) cc_final: 0.4816 (tt) outliers start: 43 outliers final: 29 residues processed: 323 average time/residue: 0.1442 time to fit residues: 71.3138 Evaluate side-chains 324 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 290 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 711 MET Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 820 GLN Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1197 GLU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 240 optimal weight: 0.0040 chunk 141 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN A 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.193082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.167266 restraints weight = 28723.585| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 2.97 r_work: 0.4198 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19106 Z= 0.147 Angle : 0.665 16.219 25861 Z= 0.330 Chirality : 0.041 0.234 3088 Planarity : 0.004 0.049 3294 Dihedral : 3.766 25.459 2624 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.15 % Allowed : 20.22 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.17), residues: 2429 helix: 1.28 (0.14), residues: 1436 sheet: -1.86 (1.11), residues: 22 loop : -1.55 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 191 TYR 0.028 0.002 TYR A 244 PHE 0.039 0.002 PHE A 232 TRP 0.023 0.002 TRP C 933 HIS 0.019 0.001 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (19096) covalent geometry : angle 0.66481 / 0.33 (25858) hydrogen bonds : bond 0.03790 / 2.46 ( 1014) hydrogen bonds : angle 4.21608 / 2.93 ( 3012) metal coordination : bond 0.01038 / 0.62 ( 10) metal coordination : angle 0.73404 / 0.43 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.7250 (mpp) cc_final: 0.7001 (mpp) REVERT: A 139 TYR cc_start: 0.7250 (t80) cc_final: 0.6816 (t80) REVERT: A 259 GLU cc_start: 0.7545 (tp30) cc_final: 0.7087 (tp30) REVERT: A 260 TYR cc_start: 0.6238 (t80) cc_final: 0.5957 (t80) REVERT: A 335 GLU cc_start: 0.7512 (tp30) cc_final: 0.7250 (tp30) REVERT: A 336 LEU cc_start: 0.6392 (mt) cc_final: 0.6146 (mt) REVERT: A 338 LYS cc_start: 0.7950 (tptp) cc_final: 0.7724 (tptp) REVERT: A 498 PHE cc_start: 0.6443 (t80) cc_final: 0.6196 (t80) REVERT: A 507 MET cc_start: 0.4360 (mtm) cc_final: 0.3647 (mtm) REVERT: A 705 GLU cc_start: 0.6959 (mp0) cc_final: 0.6688 (mp0) REVERT: A 774 TYR cc_start: 0.5470 (t80) cc_final: 0.4609 (t80) REVERT: C 116 GLU cc_start: 0.6793 (tp30) cc_final: 0.6538 (tp30) REVERT: C 137 ARG cc_start: 0.6924 (ttm-80) cc_final: 0.6695 (mmm-85) REVERT: C 272 ARG cc_start: 0.4961 (mpp80) cc_final: 0.4453 (ttp80) REVERT: C 403 LYS cc_start: 0.7972 (mttp) cc_final: 0.7750 (mttp) REVERT: C 517 VAL cc_start: 0.5963 (m) cc_final: 0.5728 (t) REVERT: C 650 GLU cc_start: 0.6375 (tp30) cc_final: 0.6061 (tm-30) REVERT: C 820 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6081 (tt0) REVERT: C 897 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7687 (mm-40) REVERT: C 915 GLU cc_start: 0.6362 (tp30) cc_final: 0.6134 (tp30) REVERT: C 1125 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7901 (tt) REVERT: C 1178 ARG cc_start: 0.7157 (ttm170) cc_final: 0.6752 (mtm-85) REVERT: C 1197 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6063 (mt-10) REVERT: E 123 VAL cc_start: 0.7742 (m) cc_final: 0.7512 (m) REVERT: E 133 ASP cc_start: 0.6775 (m-30) cc_final: 0.6502 (m-30) REVERT: E 147 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6611 (mm) REVERT: E 235 LEU cc_start: 0.5280 (OUTLIER) cc_final: 0.4937 (tt) outliers start: 42 outliers final: 30 residues processed: 319 average time/residue: 0.1475 time to fit residues: 72.0636 Evaluate side-chains 328 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 293 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 711 MET Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 820 GLN Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1131 SER Chi-restraints excluded: chain C residue 1197 GLU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 117 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 95 optimal weight: 0.0170 chunk 241 optimal weight: 0.9980 chunk 172 optimal weight: 0.7980 chunk 223 optimal weight: 7.9990 chunk 99 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 HIS A 255 ASN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.193691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.168020 restraints weight = 28859.773| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 2.96 r_work: 0.4204 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19106 Z= 0.137 Angle : 0.657 15.764 25861 Z= 0.326 Chirality : 0.041 0.223 3088 Planarity : 0.004 0.054 3294 Dihedral : 3.768 24.850 2624 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.15 % Allowed : 20.42 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2429 helix: 1.28 (0.14), residues: 1440 sheet: -1.85 (1.11), residues: 22 loop : -1.51 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 191 TYR 0.034 0.002 TYR A 278 PHE 0.029 0.002 PHE C 282 TRP 0.020 0.002 TRP C 933 HIS 0.029 0.001 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (19096) covalent geometry : angle 0.65732 / 0.33 (25858) hydrogen bonds : bond 0.03601 / 2.34 ( 1014) hydrogen bonds : angle 4.23202 / 2.95 ( 3012) metal coordination : bond 0.00922 / 0.58 ( 10) metal coordination : angle 0.69790 / 0.38 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6517.70 seconds wall clock time: 111 minutes 41.00 seconds (6701.00 seconds total)