Starting phenix.real_space_refine on Sat Sep 28 08:28:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or0_17114/09_2024/8or0_17114.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or0_17114/09_2024/8or0_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or0_17114/09_2024/8or0_17114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or0_17114/09_2024/8or0_17114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or0_17114/09_2024/8or0_17114.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or0_17114/09_2024/8or0_17114.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 12, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 8, 'GLU:plan': 10, 'ARG:plan': 7} 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, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 4, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 6} 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: 10.75, per 1000 atoms: 0.57 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: 5.02 Conformation dependent library (CDL) restraints added in 2.4 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: 2.08 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: 6.41 Time building geometry restraints manager: 5.48 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: 1.590 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: 0.750 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 45.530 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5479 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 19096 Z= 0.257 Angle : 0.638 16.173 25858 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 : 6.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.001 TRP A 545 HIS 0.012 0.001 HIS A 343 PHE 0.026 0.001 PHE A 402 TYR 0.016 0.001 TYR C 291 ARG 0.008 0.000 ARG C 382 *********************** 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 fitting. rotamer outliers: 10 poor density : 282 time to evaluate : 2.057 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: 0.3306 time to fit residues: 145.0914 Evaluate side-chains 278 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 270 time to evaluate : 2.298 ------------------------------------------------------------------------------- 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 206 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 103 optimal weight: 0.2980 chunk 63 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 192 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 142 optimal weight: 0.7980 chunk 222 optimal weight: 20.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 304 HIS ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN A 696 GLN 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5817 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 19096 Z= 0.219 Angle : 0.591 9.623 25858 Z= 0.300 Chirality : 0.040 0.149 3088 Planarity : 0.004 0.060 3294 Dihedral : 5.027 149.522 2642 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.10 % Allowed : 12.78 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2429 helix: 1.67 (0.14), residues: 1448 sheet: -2.50 (1.08), residues: 22 loop : -1.77 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 933 HIS 0.009 0.001 HIS B 77 PHE 0.024 0.002 PHE C 282 TYR 0.014 0.002 TYR A 278 ARG 0.007 0.001 ARG A 473 *********************** 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 339 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 298 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 GLU cc_start: 0.6502 (pp20) cc_final: 0.6192 (pt0) REVERT: A 323 TYR cc_start: 0.7790 (t80) cc_final: 0.7520 (t80) REVERT: A 705 GLU cc_start: 0.7118 (mp0) cc_final: 0.6834 (mp0) REVERT: C 158 MET cc_start: 0.5567 (mmm) cc_final: 0.5327 (tpt) REVERT: C 905 ARG cc_start: 0.4517 (ttt-90) cc_final: 0.3909 (ttt90) REVERT: C 945 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6960 (tm-30) REVERT: C 1054 ASN cc_start: 0.6991 (t0) cc_final: 0.6733 (t0) REVERT: C 1068 MET cc_start: 0.2182 (mtt) cc_final: 0.1593 (tpt) REVERT: C 1118 ASP cc_start: 0.5613 (p0) cc_final: 0.5405 (p0) REVERT: C 1169 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7256 (mt0) REVERT: C 1177 MET cc_start: 0.6861 (mmp) cc_final: 0.6578 (mmm) REVERT: C 1197 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.5296 (pt0) REVERT: D 165 TRP cc_start: 0.5157 (p-90) cc_final: 0.4895 (p-90) REVERT: E 235 LEU cc_start: 0.4093 (OUTLIER) cc_final: 0.3797 (tt) outliers start: 41 outliers final: 18 residues processed: 321 average time/residue: 0.3106 time to fit residues: 151.9276 Evaluate side-chains 301 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 281 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 302 ILE 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 84 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 581 ILE 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 C residue 1197 GLU 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 96 SER Chi-restraints excluded: chain E residue 109 PHE 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 123 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 185 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 222 optimal weight: 30.0000 chunk 240 optimal weight: 0.0170 chunk 198 optimal weight: 3.9990 chunk 221 optimal weight: 0.0060 chunk 75 optimal weight: 0.0010 chunk 178 optimal weight: 0.9980 overall best weight: 0.3240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 19096 Z= 0.162 Angle : 0.537 9.099 25858 Z= 0.269 Chirality : 0.039 0.328 3088 Planarity : 0.004 0.051 3294 Dihedral : 3.503 54.415 2625 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.21 % Allowed : 14.42 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2429 helix: 1.71 (0.14), residues: 1446 sheet: -2.19 (1.11), residues: 22 loop : -1.71 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 933 HIS 0.009 0.001 HIS A 343 PHE 0.026 0.001 PHE A 402 TYR 0.016 0.001 TYR A 278 ARG 0.004 0.000 ARG C1129 *********************** 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 344 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 301 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 PHE cc_start: 0.6994 (t80) cc_final: 0.6744 (t80) REVERT: A 244 TYR cc_start: 0.6755 (m-80) cc_final: 0.6373 (m-80) REVERT: A 317 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6634 (tm-30) REVERT: A 323 TYR cc_start: 0.7780 (t80) cc_final: 0.7520 (t80) REVERT: A 375 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6884 (ttpp) REVERT: A 688 MET cc_start: 0.5050 (OUTLIER) cc_final: 0.4671 (tpp) REVERT: A 705 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: C 66 ASN cc_start: 0.7238 (t0) cc_final: 0.6948 (t0) REVERT: C 446 LYS cc_start: 0.7442 (mmpt) cc_final: 0.7185 (mmpt) REVERT: C 517 VAL cc_start: 0.6583 (m) cc_final: 0.6343 (t) REVERT: C 711 MET cc_start: 0.6113 (mtp) cc_final: 0.5829 (mtp) REVERT: C 905 ARG cc_start: 0.4642 (ttt-90) cc_final: 0.4175 (ttt90) REVERT: C 1118 ASP cc_start: 0.5519 (p0) cc_final: 0.5307 (p0) REVERT: C 1125 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7774 (tt) REVERT: C 1177 MET cc_start: 0.6968 (mmp) cc_final: 0.6616 (mmm) REVERT: D 165 TRP cc_start: 0.5370 (p-90) cc_final: 0.4972 (p-90) REVERT: E 123 VAL cc_start: 0.7565 (m) cc_final: 0.7317 (m) REVERT: E 133 ASP cc_start: 0.6662 (m-30) cc_final: 0.6441 (m-30) REVERT: E 217 ARG cc_start: 0.6688 (mmm160) cc_final: 0.6227 (tpm170) REVERT: E 235 LEU cc_start: 0.4057 (OUTLIER) cc_final: 0.3771 (tt) outliers start: 43 outliers final: 24 residues processed: 325 average time/residue: 0.2875 time to fit residues: 143.6172 Evaluate side-chains 310 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 281 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 375 LYS 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 A residue 688 MET Chi-restraints excluded: chain A residue 705 GLU 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 247 HIS Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 763 VAL 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 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 147 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 149 optimal weight: 0.0070 chunk 223 optimal weight: 50.0000 chunk 236 optimal weight: 7.9990 chunk 116 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN A 538 GLN A 737 GLN C 404 GLN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 911 HIS C1036 ASN C1160 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19096 Z= 0.247 Angle : 0.639 9.394 25858 Z= 0.323 Chirality : 0.042 0.284 3088 Planarity : 0.004 0.051 3294 Dihedral : 3.928 42.895 2625 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.49 % Allowed : 14.78 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2429 helix: 1.27 (0.14), residues: 1441 sheet: -2.32 (1.07), residues: 22 loop : -1.72 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 94 HIS 0.020 0.002 HIS D 64 PHE 0.028 0.002 PHE C 282 TYR 0.023 0.002 TYR C 304 ARG 0.007 0.001 ARG C 948 *********************** 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 386 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 318 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLU cc_start: 0.7209 (tp30) cc_final: 0.6809 (tp30) REVERT: A 323 TYR cc_start: 0.7902 (t80) cc_final: 0.7562 (t80) REVERT: A 335 GLU cc_start: 0.6911 (tp30) cc_final: 0.6574 (tp30) REVERT: A 338 LYS cc_start: 0.7698 (tptp) cc_final: 0.7451 (tptp) REVERT: A 411 MET cc_start: 0.5662 (ppp) cc_final: 0.4798 (ptp) REVERT: A 469 MET cc_start: 0.4643 (mmt) cc_final: 0.4259 (mmt) REVERT: A 774 TYR cc_start: 0.5452 (t80) cc_final: 0.4682 (t80) REVERT: C 83 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6677 (pm20) REVERT: C 231 THR cc_start: 0.1630 (OUTLIER) cc_final: 0.1276 (m) REVERT: C 254 GLU cc_start: 0.6613 (mp0) cc_final: 0.6242 (mp0) REVERT: C 446 LYS cc_start: 0.7674 (mmpt) cc_final: 0.7451 (mmpt) REVERT: C 517 VAL cc_start: 0.6637 (m) cc_final: 0.6358 (t) REVERT: C 713 ILE cc_start: 0.6615 (pt) cc_final: 0.6378 (mm) REVERT: C 799 ILE cc_start: 0.4807 (OUTLIER) cc_final: 0.4576 (tp) REVERT: C 820 GLN cc_start: 0.5978 (OUTLIER) cc_final: 0.5263 (tt0) REVERT: C 847 HIS cc_start: 0.5410 (OUTLIER) cc_final: 0.4839 (t70) REVERT: C 897 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7305 (mm-40) REVERT: C 905 ARG cc_start: 0.5836 (ttt-90) cc_final: 0.5255 (ttt90) REVERT: C 1087 GLU cc_start: 0.6039 (mm-30) cc_final: 0.5826 (mm-30) REVERT: C 1125 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7892 (tt) REVERT: C 1177 MET cc_start: 0.7419 (mmp) cc_final: 0.7146 (mmm) REVERT: C 1178 ARG cc_start: 0.7134 (ttm170) cc_final: 0.6627 (mtm-85) REVERT: C 1197 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.5795 (mt-10) REVERT: D 4 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7432 (mp) REVERT: D 165 TRP cc_start: 0.5704 (p-90) cc_final: 0.5075 (p-90) REVERT: E 123 VAL cc_start: 0.7710 (m) cc_final: 0.7437 (m) REVERT: E 133 ASP cc_start: 0.6886 (m-30) cc_final: 0.6592 (m-30) REVERT: E 235 LEU cc_start: 0.4822 (OUTLIER) cc_final: 0.4492 (tt) outliers start: 68 outliers final: 33 residues processed: 350 average time/residue: 0.3201 time to fit residues: 168.4328 Evaluate side-chains 352 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 310 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN 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 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 490 SER Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 GLN Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 931 ASN Chi-restraints excluded: chain C residue 980 TYR Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 994 SER 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 C residue 1199 GLN Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 106 LEU 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 160 VAL 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 197 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 chunk 176 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 202 optimal weight: 0.4980 chunk 163 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 120 optimal weight: 0.0570 chunk 212 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN C 429 GLN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN D 49 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19096 Z= 0.189 Angle : 0.577 9.519 25858 Z= 0.292 Chirality : 0.040 0.284 3088 Planarity : 0.004 0.048 3294 Dihedral : 3.778 43.937 2625 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.03 % Allowed : 16.42 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2429 helix: 1.38 (0.14), residues: 1434 sheet: -2.26 (1.07), residues: 22 loop : -1.72 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 94 HIS 0.012 0.001 HIS A 343 PHE 0.032 0.002 PHE A 243 TYR 0.022 0.002 TYR A 244 ARG 0.007 0.001 ARG A 191 *********************** 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 370 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 311 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 GLU cc_start: 0.6990 (tp30) cc_final: 0.6620 (tp30) REVERT: A 338 LYS cc_start: 0.7684 (tptp) cc_final: 0.7440 (tptp) REVERT: A 378 ASN cc_start: 0.6996 (t0) cc_final: 0.6784 (t0) REVERT: A 411 MET cc_start: 0.5800 (ppp) cc_final: 0.5111 (ptp) REVERT: A 774 TYR cc_start: 0.5524 (t80) cc_final: 0.4739 (t80) REVERT: C 231 THR cc_start: 0.1540 (OUTLIER) cc_final: 0.1098 (p) REVERT: C 446 LYS cc_start: 0.7645 (mmpt) cc_final: 0.7416 (mmpt) REVERT: C 517 VAL cc_start: 0.6456 (m) cc_final: 0.6207 (t) REVERT: C 711 MET cc_start: 0.6528 (mtp) cc_final: 0.6281 (mtp) REVERT: C 799 ILE cc_start: 0.4747 (OUTLIER) cc_final: 0.4518 (tp) REVERT: C 820 GLN cc_start: 0.6117 (OUTLIER) cc_final: 0.5535 (tt0) REVERT: C 847 HIS cc_start: 0.5486 (OUTLIER) cc_final: 0.4770 (t70) REVERT: C 857 LEU cc_start: 0.1181 (OUTLIER) cc_final: 0.0809 (tt) REVERT: C 897 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7320 (mm-40) REVERT: C 905 ARG cc_start: 0.6044 (ttt-90) cc_final: 0.5398 (ttt90) REVERT: C 1125 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7849 (tt) REVERT: C 1197 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.5600 (mt-10) REVERT: D 4 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7496 (mp) REVERT: D 7 GLN cc_start: 0.5299 (tp40) cc_final: 0.5052 (tp40) REVERT: E 123 VAL cc_start: 0.7658 (m) cc_final: 0.7421 (m) REVERT: E 133 ASP cc_start: 0.6923 (m-30) cc_final: 0.6653 (m-30) REVERT: E 235 LEU cc_start: 0.4840 (OUTLIER) cc_final: 0.4514 (tt) outliers start: 59 outliers final: 31 residues processed: 344 average time/residue: 0.3181 time to fit residues: 164.8474 Evaluate side-chains 337 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 297 time to evaluate : 1.984 ------------------------------------------------------------------------------- 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 261 MET 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 490 SER Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 GLN Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 980 TYR 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 C residue 1199 GLN 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 113 CYS Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 160 VAL 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 79 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 139 optimal weight: 0.2980 chunk 58 optimal weight: 0.0570 chunk 237 optimal weight: 0.2980 chunk 196 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 276 GLN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 GLN ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19096 Z= 0.166 Angle : 0.581 10.826 25858 Z= 0.288 Chirality : 0.040 0.271 3088 Planarity : 0.004 0.047 3294 Dihedral : 3.563 24.474 2624 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.62 % Allowed : 18.11 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2429 helix: 1.38 (0.14), residues: 1449 sheet: -2.15 (1.10), residues: 22 loop : -1.64 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 94 HIS 0.017 0.001 HIS A 343 PHE 0.036 0.001 PHE A 243 TYR 0.027 0.001 TYR A 244 ARG 0.012 0.000 ARG C 351 *********************** 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 356 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 305 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 TYR cc_start: 0.6551 (m-80) cc_final: 0.6245 (m-80) REVERT: A 260 TYR cc_start: 0.5848 (t80) cc_final: 0.5647 (t80) REVERT: A 323 TYR cc_start: 0.7866 (t80) cc_final: 0.7646 (t80) REVERT: A 335 GLU cc_start: 0.7122 (tp30) cc_final: 0.6710 (tp30) REVERT: A 338 LYS cc_start: 0.7638 (tptp) cc_final: 0.7407 (tptp) REVERT: A 378 ASN cc_start: 0.6950 (t0) cc_final: 0.6727 (t0) REVERT: A 411 MET cc_start: 0.5843 (ppp) cc_final: 0.5245 (ptp) REVERT: A 633 MET cc_start: 0.5624 (tpp) cc_final: 0.5264 (tpp) REVERT: A 688 MET cc_start: 0.5063 (OUTLIER) cc_final: 0.4655 (tpp) REVERT: A 774 TYR cc_start: 0.5452 (t80) cc_final: 0.4700 (t80) REVERT: C 181 LEU cc_start: 0.7604 (mm) cc_final: 0.7266 (mp) REVERT: C 203 VAL cc_start: 0.7917 (t) cc_final: 0.7616 (m) REVERT: C 231 THR cc_start: 0.1572 (OUTLIER) cc_final: 0.1182 (p) REVERT: C 446 LYS cc_start: 0.7641 (mmpt) cc_final: 0.7413 (mmpt) REVERT: C 517 VAL cc_start: 0.6447 (m) cc_final: 0.6203 (t) REVERT: C 650 GLU cc_start: 0.6245 (tp30) cc_final: 0.5827 (tm-30) REVERT: C 706 MET cc_start: 0.6806 (mmt) cc_final: 0.6554 (mmm) REVERT: C 799 ILE cc_start: 0.4642 (OUTLIER) cc_final: 0.4392 (tp) REVERT: C 897 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7322 (mm-40) REVERT: C 947 THR cc_start: 0.7443 (m) cc_final: 0.7195 (p) REVERT: C 1125 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8001 (tt) REVERT: C 1197 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.5496 (mt-10) REVERT: D 7 GLN cc_start: 0.5416 (tp40) cc_final: 0.5192 (tp40) REVERT: D 165 TRP cc_start: 0.5783 (p-90) cc_final: 0.5146 (p-90) REVERT: E 123 VAL cc_start: 0.7655 (m) cc_final: 0.7419 (m) REVERT: E 133 ASP cc_start: 0.6943 (m-30) cc_final: 0.6645 (m-30) REVERT: E 235 LEU cc_start: 0.4882 (OUTLIER) cc_final: 0.4563 (tt) outliers start: 51 outliers final: 28 residues processed: 331 average time/residue: 0.3162 time to fit residues: 157.9869 Evaluate side-chains 330 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 296 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 763 VAL Chi-restraints excluded: chain C residue 799 ILE 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 C residue 1199 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 55 LEU 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 160 VAL 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 228 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 199 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 143 optimal weight: 0.3980 chunk 109 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 887 ASN ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19096 Z= 0.220 Angle : 0.620 10.188 25858 Z= 0.310 Chirality : 0.041 0.271 3088 Planarity : 0.004 0.047 3294 Dihedral : 3.710 24.166 2624 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.72 % Allowed : 18.27 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2429 helix: 1.32 (0.14), residues: 1439 sheet: -2.17 (1.06), residues: 22 loop : -1.65 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 94 HIS 0.017 0.001 HIS A 343 PHE 0.049 0.002 PHE A 498 TYR 0.026 0.002 TYR A 244 ARG 0.008 0.001 ARG A 191 *********************** 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 351 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 298 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.7092 (t80) cc_final: 0.6534 (t80) REVERT: A 260 TYR cc_start: 0.6036 (t80) cc_final: 0.5812 (t80) REVERT: A 323 TYR cc_start: 0.7891 (t80) cc_final: 0.7685 (t80) REVERT: A 335 GLU cc_start: 0.7271 (tp30) cc_final: 0.6888 (tp30) REVERT: A 338 LYS cc_start: 0.7663 (tptp) cc_final: 0.7443 (tptp) REVERT: A 377 TYR cc_start: 0.6169 (m-10) cc_final: 0.5643 (m-10) REVERT: A 378 ASN cc_start: 0.7152 (t0) cc_final: 0.6793 (t0) REVERT: A 382 MET cc_start: 0.6946 (mmm) cc_final: 0.6648 (tpp) REVERT: A 411 MET cc_start: 0.6007 (ppp) cc_final: 0.5759 (ptp) REVERT: A 688 MET cc_start: 0.5241 (tpt) cc_final: 0.4870 (tpp) REVERT: A 774 TYR cc_start: 0.5634 (t80) cc_final: 0.4768 (t80) REVERT: C 83 GLN cc_start: 0.7038 (pm20) cc_final: 0.6784 (pm20) REVERT: C 231 THR cc_start: 0.1454 (OUTLIER) cc_final: 0.0988 (p) REVERT: C 517 VAL cc_start: 0.6348 (m) cc_final: 0.6134 (t) REVERT: C 650 GLU cc_start: 0.6188 (tp30) cc_final: 0.5814 (tm-30) REVERT: C 756 LEU cc_start: 0.6288 (mt) cc_final: 0.5824 (mp) REVERT: C 799 ILE cc_start: 0.4691 (OUTLIER) cc_final: 0.4480 (tp) REVERT: C 820 GLN cc_start: 0.6292 (OUTLIER) cc_final: 0.5731 (mt0) REVERT: C 847 HIS cc_start: 0.5626 (OUTLIER) cc_final: 0.4789 (t70) REVERT: C 897 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7484 (mm-40) REVERT: C 947 THR cc_start: 0.7482 (m) cc_final: 0.7239 (p) REVERT: C 1125 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7983 (tt) REVERT: C 1178 ARG cc_start: 0.7060 (ttm170) cc_final: 0.6616 (mtt-85) REVERT: C 1197 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.5751 (mt-10) REVERT: D 7 GLN cc_start: 0.5800 (tp40) cc_final: 0.5527 (tp40) REVERT: E 123 VAL cc_start: 0.7680 (m) cc_final: 0.7442 (m) REVERT: E 133 ASP cc_start: 0.6821 (m-30) cc_final: 0.6584 (m-30) REVERT: E 235 LEU cc_start: 0.5031 (OUTLIER) cc_final: 0.4702 (tt) outliers start: 53 outliers final: 34 residues processed: 329 average time/residue: 0.3037 time to fit residues: 151.4581 Evaluate side-chains 331 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 290 time to evaluate : 2.052 ------------------------------------------------------------------------------- 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 261 MET 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 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 735 LEU Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 GLN Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 931 ASN 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 C residue 1199 GLN Chi-restraints excluded: chain D residue 45 VAL 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 156 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 116 optimal weight: 0.0370 chunk 22 optimal weight: 0.6980 chunk 185 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 255 ASN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19096 Z= 0.215 Angle : 0.627 14.512 25858 Z= 0.313 Chirality : 0.041 0.263 3088 Planarity : 0.004 0.048 3294 Dihedral : 3.744 23.269 2624 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.82 % Allowed : 18.42 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2429 helix: 1.25 (0.14), residues: 1440 sheet: -2.08 (1.09), residues: 22 loop : -1.67 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 94 HIS 0.012 0.001 HIS A 343 PHE 0.040 0.002 PHE A 498 TYR 0.022 0.002 TYR A 244 ARG 0.008 0.000 ARG C 382 *********************** 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 fitting. rotamer outliers: 55 poor density : 304 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.7124 (t80) cc_final: 0.6565 (t80) REVERT: A 260 TYR cc_start: 0.6072 (t80) cc_final: 0.5871 (t80) REVERT: A 286 GLU cc_start: 0.7111 (pt0) cc_final: 0.6894 (pt0) REVERT: A 335 GLU cc_start: 0.7397 (tp30) cc_final: 0.6988 (tp30) REVERT: A 338 LYS cc_start: 0.7676 (tptp) cc_final: 0.7465 (tptp) REVERT: A 688 MET cc_start: 0.5286 (OUTLIER) cc_final: 0.5081 (tpp) REVERT: A 774 TYR cc_start: 0.5528 (t80) cc_final: 0.4696 (t80) REVERT: C 30 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6409 (tt) REVERT: C 83 GLN cc_start: 0.7057 (pm20) cc_final: 0.6795 (pm20) REVERT: C 279 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.6231 (p90) REVERT: C 403 LYS cc_start: 0.7940 (mttp) cc_final: 0.7647 (mttp) REVERT: C 650 GLU cc_start: 0.6208 (tp30) cc_final: 0.5853 (tm-30) REVERT: C 799 ILE cc_start: 0.4607 (OUTLIER) cc_final: 0.4390 (tp) REVERT: C 820 GLN cc_start: 0.6422 (OUTLIER) cc_final: 0.5819 (tt0) REVERT: C 847 HIS cc_start: 0.5829 (OUTLIER) cc_final: 0.4740 (t70) REVERT: C 850 ASP cc_start: 0.7528 (t0) cc_final: 0.7278 (t0) REVERT: C 897 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7453 (mm-40) REVERT: C 1125 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7987 (tt) REVERT: C 1178 ARG cc_start: 0.7078 (ttm170) cc_final: 0.6636 (mtt180) REVERT: C 1197 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.5718 (mt-10) REVERT: D 7 GLN cc_start: 0.5923 (tp40) cc_final: 0.5642 (tp40) REVERT: D 165 TRP cc_start: 0.6177 (p-90) cc_final: 0.5397 (p-90) REVERT: E 123 VAL cc_start: 0.7698 (m) cc_final: 0.7456 (m) REVERT: E 133 ASP cc_start: 0.6840 (m-30) cc_final: 0.6541 (m-30) REVERT: E 235 LEU cc_start: 0.5202 (OUTLIER) cc_final: 0.4876 (tt) outliers start: 55 outliers final: 35 residues processed: 334 average time/residue: 0.3124 time to fit residues: 157.5435 Evaluate side-chains 334 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 290 time to evaluate : 1.944 ------------------------------------------------------------------------------- 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 261 MET 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 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 30 LEU 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 279 PHE 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 763 VAL Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 GLN Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 931 ASN 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 C residue 1199 GLN Chi-restraints excluded: chain D residue 45 VAL 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 D residue 162 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 156 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 10.0000 chunk 226 optimal weight: 30.0000 chunk 206 optimal weight: 0.9980 chunk 220 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 172 optimal weight: 0.1980 chunk 67 optimal weight: 4.9990 chunk 198 optimal weight: 0.0970 chunk 208 optimal weight: 0.9980 chunk 219 optimal weight: 8.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN C 748 GLN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 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 : 0.004 0.048 19096 Z= 0.232 Angle : 0.671 19.071 25858 Z= 0.332 Chirality : 0.042 0.263 3088 Planarity : 0.004 0.048 3294 Dihedral : 3.861 23.099 2624 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.77 % Allowed : 19.39 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2429 helix: 1.18 (0.14), residues: 1437 sheet: -2.01 (1.10), residues: 22 loop : -1.67 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 933 HIS 0.030 0.001 HIS A 343 PHE 0.045 0.002 PHE A 498 TYR 0.031 0.002 TYR C1117 ARG 0.006 0.000 ARG A 191 *********************** 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 351 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 297 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.3331 (ppp) cc_final: 0.2785 (ppp) REVERT: A 139 TYR cc_start: 0.7158 (t80) cc_final: 0.6631 (t80) REVERT: A 335 GLU cc_start: 0.7427 (tp30) cc_final: 0.7015 (tp30) REVERT: A 336 LEU cc_start: 0.6437 (mt) cc_final: 0.6236 (mt) REVERT: A 338 LYS cc_start: 0.7705 (tptp) cc_final: 0.7471 (tptp) REVERT: A 688 MET cc_start: 0.5361 (OUTLIER) cc_final: 0.5149 (tpp) REVERT: A 774 TYR cc_start: 0.5612 (t80) cc_final: 0.4744 (t80) REVERT: C 83 GLN cc_start: 0.7007 (pm20) cc_final: 0.6767 (pm20) REVERT: C 254 GLU cc_start: 0.6290 (mp0) cc_final: 0.6077 (mp0) REVERT: C 279 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.6226 (p90) REVERT: C 403 LYS cc_start: 0.7946 (mttp) cc_final: 0.7721 (mttp) REVERT: C 799 ILE cc_start: 0.4529 (OUTLIER) cc_final: 0.4329 (tp) REVERT: C 807 THR cc_start: 0.7523 (OUTLIER) cc_final: 0.7137 (p) REVERT: C 820 GLN cc_start: 0.6336 (OUTLIER) cc_final: 0.5678 (tt0) REVERT: C 847 HIS cc_start: 0.5828 (OUTLIER) cc_final: 0.4757 (t70) REVERT: C 850 ASP cc_start: 0.7564 (t0) cc_final: 0.7253 (t0) REVERT: C 897 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7464 (mm-40) REVERT: C 915 GLU cc_start: 0.6149 (tp30) cc_final: 0.5943 (tp30) REVERT: C 1125 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7994 (tt) REVERT: C 1178 ARG cc_start: 0.7102 (ttm170) cc_final: 0.6700 (mtm-85) REVERT: C 1197 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.5674 (mt-10) REVERT: D 7 GLN cc_start: 0.6074 (tp40) cc_final: 0.5757 (tp40) REVERT: D 165 TRP cc_start: 0.6246 (p-90) cc_final: 0.5466 (p-90) REVERT: E 123 VAL cc_start: 0.7709 (m) cc_final: 0.7471 (m) REVERT: E 130 LEU cc_start: 0.7392 (mm) cc_final: 0.7167 (mm) REVERT: E 133 ASP cc_start: 0.6833 (m-30) cc_final: 0.6484 (m-30) REVERT: E 235 LEU cc_start: 0.5337 (OUTLIER) cc_final: 0.4997 (tt) outliers start: 54 outliers final: 36 residues processed: 327 average time/residue: 0.3191 time to fit residues: 158.4839 Evaluate side-chains 332 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 287 time to evaluate : 2.089 ------------------------------------------------------------------------------- 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 371 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 585 LEU 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 110 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 279 PHE 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 748 GLN Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 820 GLN Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 931 ASN 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 C residue 1199 GLN Chi-restraints excluded: chain D residue 45 VAL 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 D residue 162 GLU 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 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 144 optimal weight: 0.9980 chunk 232 optimal weight: 2.9990 chunk 142 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 chunk 244 optimal weight: 10.0000 chunk 224 optimal weight: 40.0000 chunk 194 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 150 optimal weight: 0.0980 chunk 119 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 255 ASN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 GLN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19096 Z= 0.227 Angle : 0.682 21.042 25858 Z= 0.335 Chirality : 0.043 0.292 3088 Planarity : 0.004 0.054 3294 Dihedral : 3.874 22.586 2624 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.62 % Allowed : 19.81 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2429 helix: 1.10 (0.14), residues: 1440 sheet: -2.00 (1.10), residues: 22 loop : -1.65 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 94 HIS 0.026 0.001 HIS A 343 PHE 0.044 0.002 PHE A 498 TYR 0.032 0.002 TYR C1117 ARG 0.009 0.001 ARG A 191 ********************** 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 342 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 291 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.3446 (ppp) cc_final: 0.2877 (ppp) REVERT: A 139 TYR cc_start: 0.7133 (t80) cc_final: 0.6605 (t80) REVERT: A 335 GLU cc_start: 0.7478 (tp30) cc_final: 0.7213 (tp30) REVERT: A 338 LYS cc_start: 0.7701 (tptp) cc_final: 0.7440 (tptp) REVERT: A 507 MET cc_start: 0.4097 (mtm) cc_final: 0.3278 (mtm) REVERT: A 589 GLU cc_start: 0.6038 (pm20) cc_final: 0.5748 (pm20) REVERT: A 705 GLU cc_start: 0.7154 (mp0) cc_final: 0.6941 (mp0) REVERT: A 774 TYR cc_start: 0.5680 (t80) cc_final: 0.4792 (t80) REVERT: C 83 GLN cc_start: 0.7003 (pm20) cc_final: 0.6747 (pm20) REVERT: C 279 PHE cc_start: 0.6521 (OUTLIER) cc_final: 0.6247 (p90) REVERT: C 287 PRO cc_start: 0.7276 (Cg_endo) cc_final: 0.7047 (Cg_exo) REVERT: C 351 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.7194 (mtm-85) REVERT: C 403 LYS cc_start: 0.7941 (mttp) cc_final: 0.7723 (mttp) REVERT: C 799 ILE cc_start: 0.4679 (OUTLIER) cc_final: 0.4459 (tp) REVERT: C 807 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.7103 (p) REVERT: C 820 GLN cc_start: 0.6310 (OUTLIER) cc_final: 0.5871 (mt0) REVERT: C 847 HIS cc_start: 0.5803 (OUTLIER) cc_final: 0.4688 (t70) REVERT: C 850 ASP cc_start: 0.7557 (t0) cc_final: 0.7270 (t0) REVERT: C 1125 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7977 (tt) REVERT: C 1178 ARG cc_start: 0.7097 (ttm170) cc_final: 0.6686 (mtt90) REVERT: C 1197 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.5697 (mt-10) REVERT: E 123 VAL cc_start: 0.7704 (m) cc_final: 0.7463 (m) REVERT: E 130 LEU cc_start: 0.7352 (mm) cc_final: 0.7133 (mm) REVERT: E 133 ASP cc_start: 0.6891 (m-30) cc_final: 0.6511 (m-30) REVERT: E 235 LEU cc_start: 0.5407 (OUTLIER) cc_final: 0.5066 (tt) outliers start: 51 outliers final: 36 residues processed: 319 average time/residue: 0.3092 time to fit residues: 150.5424 Evaluate side-chains 326 residues out of total 2254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 282 time to evaluate : 1.906 ------------------------------------------------------------------------------- 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 300 LEU Chi-restraints excluded: chain A residue 371 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 279 PHE 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 763 VAL Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 820 GLN Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 931 ASN 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 1171 GLU Chi-restraints excluded: chain C residue 1197 GLU Chi-restraints excluded: chain C residue 1199 GLN Chi-restraints excluded: chain D residue 45 VAL 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 D residue 162 GLU 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 156 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 154 optimal weight: 0.0070 chunk 207 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 179 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 54 optimal weight: 0.3980 chunk 194 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 GLN A 737 GLN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.192199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.166930 restraints weight = 28632.672| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 2.90 r_work: 0.4199 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19096 Z= 0.198 Angle : 0.660 20.566 25858 Z= 0.325 Chirality : 0.042 0.255 3088 Planarity : 0.004 0.047 3294 Dihedral : 3.763 21.765 2624 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.46 % Allowed : 19.96 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2429 helix: 1.12 (0.14), residues: 1445 sheet: -2.02 (1.10), residues: 22 loop : -1.62 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 94 HIS 0.023 0.001 HIS A 343 PHE 0.043 0.002 PHE A 498 TYR 0.025 0.002 TYR A 244 ARG 0.009 0.001 ARG A 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4606.07 seconds wall clock time: 83 minutes 35.76 seconds (5015.76 seconds total)