Starting phenix.real_space_refine on Sun Aug 24 09:24:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8or0_17114/08_2025/8or0_17114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8or0_17114/08_2025/8or0_17114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8or0_17114/08_2025/8or0_17114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8or0_17114/08_2025/8or0_17114.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8or0_17114/08_2025/8or0_17114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8or0_17114/08_2025/8or0_17114.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 104 5.16 5 C 11921 2.51 5 N 3254 2.21 5 O 3541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18823 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5531 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 663} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 731 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 8847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1137, 8847 Classifications: {'peptide': 1137} Link IDs: {'PTRANS': 54, 'TRANS': 1082} Chain breaks: 6 Chain: "D" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain breaks: 3 Chain: "E" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 1899 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PTRANS': 13, 'TRANS': 293} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 563 Unresolved non-hydrogen angles: 726 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 10, 'PHE:plan': 8, 'GLN:plan1': 12, 'ARG:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 2, 'HIS:plan': 6, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 294 Chain: "G" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 319 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 5, 'ASP:plan': 4, 'GLU:plan': 7, 'PHE:plan': 2, 'ARG:plan': 4, 'HIS:plan': 5, 'TRP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 157 Chain: "H" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 421 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 7, 'TRANS': 77} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 4, 'TRP:plan': 4, 'TYR:plan': 5, 'ARG:plan': 6, 'ASP:plan': 5, 'PHE:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 173 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5756 SG CYS B 45 62.874 112.712 136.864 1.00 97.50 S ATOM 6051 SG CYS B 83 62.524 110.686 133.913 1.00 46.50 S ATOM 5980 SG CYS B 75 48.551 114.360 128.163 1.00 58.76 S ATOM 6147 SG CYS B 94 49.330 111.557 131.289 1.00 75.85 S ATOM 5823 SG CYS B 53 67.335 112.548 132.814 1.00109.50 S ATOM 5846 SG CYS B 56 69.792 110.689 130.542 1.00118.28 S ATOM 5930 SG CYS B 68 67.401 113.296 129.037 1.00 92.41 S Time building chain proxies: 3.21, per 1000 atoms: 0.17 Number of scatterers: 18823 At special positions: 0 Unit cell: (117.72, 177.12, 153.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 104 16.00 O 3541 8.00 N 3254 7.00 C 11921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 552.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B4001 " pdb="ZN ZN B4001 " - pdb=" SG CYS B 45 " pdb="ZN ZN B4001 " - pdb=" ND1 HIS B 80 " pdb="ZN ZN B4001 " - pdb=" SG CYS B 83 " pdb=" ZN B4002 " pdb="ZN ZN B4002 " - pdb=" SG CYS B 75 " pdb="ZN ZN B4002 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B4002 " - pdb=" SG CYS B 94 " pdb=" ZN B4003 " pdb="ZN ZN B4003 " - pdb=" ND1 HIS B 82 " pdb="ZN ZN B4003 " - pdb=" SG CYS B 56 " pdb="ZN ZN B4003 " - pdb=" SG CYS B 53 " pdb="ZN ZN B4003 " - pdb=" SG CYS B 68 " Number of angles added : 3 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4798 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 8 sheets defined 65.2% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 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: 2.56 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3204 1.31 - 1.43: 4547 1.43 - 1.56: 11190 1.56 - 1.69: 3 1.69 - 1.82: 152 Bond restraints: 19096 Sorted by residual: bond pdb=" N LYS C1156 " pdb=" CA LYS C1156 " ideal model delta sigma weight residual 1.456 1.376 0.080 1.21e-02 6.83e+03 4.39e+01 bond pdb=" N THR C1154 " pdb=" CA THR C1154 " ideal model delta sigma weight residual 1.463 1.382 0.081 1.31e-02 5.83e+03 3.81e+01 bond pdb=" CA THR C1155 " pdb=" C THR C1155 " ideal model delta sigma weight residual 1.521 1.452 0.069 1.19e-02 7.06e+03 3.35e+01 bond pdb=" CA VAL C1157 " pdb=" C VAL C1157 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.14e-02 7.69e+03 3.12e+01 bond pdb=" CA VAL C1162 " pdb=" CB VAL C1162 " ideal model delta sigma weight residual 1.538 1.486 0.053 9.80e-03 1.04e+04 2.89e+01 ... (remaining 19091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 25698 3.23 - 6.47: 136 6.47 - 9.70: 17 9.70 - 12.94: 5 12.94 - 16.17: 2 Bond angle restraints: 25858 Sorted by residual: angle pdb=" CA PRO C1206 " pdb=" N PRO C1206 " pdb=" CD PRO C1206 " ideal model delta sigma weight residual 112.00 95.83 16.17 1.40e+00 5.10e-01 1.33e+02 angle pdb=" N LYS C1163 " pdb=" CA LYS C1163 " pdb=" C LYS C1163 " ideal model delta sigma weight residual 112.34 122.20 -9.86 1.30e+00 5.92e-01 5.75e+01 angle pdb=" C GLU C1171 " pdb=" N LEU C1172 " pdb=" CA LEU C1172 " ideal model delta sigma weight residual 120.58 107.75 12.83 1.71e+00 3.42e-01 5.63e+01 angle pdb=" N PRO C1206 " pdb=" CD PRO C1206 " pdb=" CG PRO C1206 " ideal model delta sigma weight residual 103.20 93.91 9.29 1.50e+00 4.44e-01 3.83e+01 angle pdb=" N THR C1154 " pdb=" CA THR C1154 " pdb=" C THR C1154 " ideal model delta sigma weight residual 111.81 103.01 8.80 1.44e+00 4.82e-01 3.74e+01 ... (remaining 25853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 10275 17.63 - 35.27: 1134 35.27 - 52.90: 256 52.90 - 70.53: 40 70.53 - 88.17: 20 Dihedral angle restraints: 11725 sinusoidal: 4404 harmonic: 7321 Sorted by residual: dihedral pdb=" N ASN C1160 " pdb=" C ASN C1160 " pdb=" CA ASN C1160 " pdb=" CB ASN C1160 " ideal model delta harmonic sigma weight residual 122.80 135.69 -12.89 0 2.50e+00 1.60e-01 2.66e+01 dihedral pdb=" CA LEU E 188 " pdb=" C LEU E 188 " pdb=" N SER E 189 " pdb=" CA SER E 189 " ideal model delta harmonic sigma weight residual 180.00 156.73 23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA SER A 231 " pdb=" C SER A 231 " pdb=" N PHE A 232 " pdb=" CA PHE A 232 " ideal model delta harmonic sigma weight residual -180.00 -158.68 -21.32 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 11722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2881 0.075 - 0.150: 195 0.150 - 0.225: 7 0.225 - 0.300: 2 0.300 - 0.375: 3 Chirality restraints: 3088 Sorted by residual: chirality pdb=" CA ASN C1160 " pdb=" N ASN C1160 " pdb=" C ASN C1160 " pdb=" CB ASN C1160 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA LYS C1163 " pdb=" N LYS C1163 " pdb=" C LYS C1163 " pdb=" CB LYS C1163 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CG LEU E 156 " pdb=" CB LEU E 156 " pdb=" CD1 LEU E 156 " pdb=" CD2 LEU E 156 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 3085 not shown) Planarity restraints: 3294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C1153 " 0.036 2.00e-02 2.50e+03 7.59e-02 5.76e+01 pdb=" C CYS C1153 " -0.131 2.00e-02 2.50e+03 pdb=" O CYS C1153 " 0.050 2.00e-02 2.50e+03 pdb=" N THR C1154 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C1205 " 0.101 5.00e-02 4.00e+02 1.39e-01 3.11e+01 pdb=" N PRO C1206 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO C1206 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO C1206 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C1162 " 0.024 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C VAL C1162 " -0.084 2.00e-02 2.50e+03 pdb=" O VAL C1162 " 0.032 2.00e-02 2.50e+03 pdb=" N LYS C1163 " 0.028 2.00e-02 2.50e+03 ... (remaining 3291 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 5 1.90 - 2.65: 214 2.65 - 3.40: 26769 3.40 - 4.15: 39574 4.15 - 4.90: 72541 Nonbonded interactions: 139103 Sorted by model distance: nonbonded pdb=" OD2 ASP C1170 " pdb=" NH2 ARG C1174 " model vdw 1.149 3.120 nonbonded pdb=" OD1 ASP C1170 " pdb=" NH1 ARG C1174 " model vdw 1.527 3.120 nonbonded pdb=" OD2 ASP C1170 " pdb=" CZ ARG C1174 " model vdw 1.722 3.270 nonbonded pdb=" OD1 ASP C1170 " pdb=" CZ ARG C1174 " model vdw 1.797 3.270 nonbonded pdb=" CG ASP C1170 " pdb=" NH1 ARG C1174 " model vdw 1.820 3.350 ... (remaining 139098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.390 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.840 ------------------------------------------------------------------------------- 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 19106 Z= 0.224 Angle : 0.638 16.173 25861 Z= 0.347 Chirality : 0.040 0.375 3088 Planarity : 0.005 0.139 3294 Dihedral : 15.612 88.167 6927 Min Nonbonded Distance : 1.149 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.51 % Allowed : 14.37 % Favored : 85.12 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.18), residues: 2429 helix: 1.84 (0.14), residues: 1431 sheet: -2.06 (0.90), residues: 33 loop : -1.86 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 382 TYR 0.016 0.001 TYR C 291 PHE 0.026 0.001 PHE A 402 TRP 0.021 0.001 TRP A 545 HIS 0.012 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00383 (19096) covalent geometry : angle 0.63815 (25858) hydrogen bonds : bond 0.12789 ( 1014) hydrogen bonds : angle 4.70249 ( 3012) metal coordination : bond 0.00720 ( 10) metal coordination : angle 0.43620 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 282 time to evaluate : 0.657 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: 0.1285 time to fit residues: 56.1898 Evaluate side-chains 278 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 270 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 994 SER Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1165 GLU Chi-restraints excluded: chain C residue 1168 LYS Chi-restraints excluded: chain C residue 1170 ASP Chi-restraints excluded: chain C residue 1171 GLU Chi-restraints excluded: chain E residue 133 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.0770 chunk 194 optimal weight: 0.0970 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0670 chunk 235 optimal weight: 6.9990 overall best weight: 0.2232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS B 92 GLN C 365 HIS C 452 GLN C 514 HIS C 911 HIS C1140 GLN C1169 GLN D 23 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.222872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.200723 restraints weight = 31583.269| |-----------------------------------------------------------------------------| r_work (start): 0.4650 rms_B_bonded: 3.05 r_work: 0.4551 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5591 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 19106 Z= 0.108 Angle : 0.523 9.479 25861 Z= 0.264 Chirality : 0.038 0.144 3088 Planarity : 0.004 0.059 3294 Dihedral : 4.674 128.407 2642 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.95 % Allowed : 12.42 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.18), residues: 2429 helix: 1.93 (0.14), residues: 1446 sheet: -2.42 (1.06), residues: 22 loop : -1.74 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1174 TYR 0.014 0.001 TYR C 291 PHE 0.024 0.001 PHE A 402 TRP 0.016 0.001 TRP C 933 HIS 0.009 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00234 (19096) covalent geometry : angle 0.52304 (25858) hydrogen bonds : bond 0.02900 ( 1014) hydrogen bonds : angle 3.79302 ( 3012) metal coordination : bond 0.00744 ( 10) metal coordination : angle 0.66036 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4858 Ramachandran restraints generated. 2429 Oldfield, 0 Emsley, 2429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 288 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLU cc_start: 0.6238 (mm-30) cc_final: 0.5990 (mm-30) REVERT: A 323 TYR cc_start: 0.7543 (t80) cc_final: 0.7292 (t80) REVERT: A 705 GLU cc_start: 0.6842 (mp0) cc_final: 0.6611 (mp0) REVERT: C 443 MET cc_start: 0.4358 (mmt) cc_final: 0.3771 (mmt) REVERT: C 654 ILE cc_start: 0.6977 (mm) cc_final: 0.6634 (tp) REVERT: C 1068 MET cc_start: 0.1917 (mtt) cc_final: 0.1367 (tpt) REVERT: C 1177 MET cc_start: 0.6558 (mmp) cc_final: 0.6265 (mmm) REVERT: E 235 LEU cc_start: 0.3898 (OUTLIER) cc_final: 0.3616 (tt) outliers start: 38 outliers final: 15 residues processed: 309 average time/residue: 0.1299 time to fit residues: 61.9815 Evaluate side-chains 301 residues out of total 2254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 285 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 1044 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.0148 > 50: distance: 21 - 24: 6.977 distance: 24 - 25: 5.904 distance: 25 - 26: 5.481 distance: 25 - 28: 8.704 distance: 26 - 27: 10.511 distance: 26 - 29: 15.095 distance: 29 - 30: 9.144 distance: 30 - 31: 14.522 distance: 30 - 33: 21.309 distance: 31 - 32: 20.052 distance: 31 - 34: 12.553 distance: 34 - 35: 12.753 distance: 35 - 36: 7.483 distance: 35 - 38: 19.971 distance: 36 - 37: 20.075 distance: 36 - 39: 12.852 distance: 39 - 40: 13.455 distance: 40 - 41: 23.758 distance: 40 - 43: 18.831 distance: 41 - 42: 21.438 distance: 41 - 44: 21.785 distance: 44 - 45: 11.252 distance: 45 - 46: 17.531 distance: 45 - 48: 20.718 distance: 46 - 47: 8.226 distance: 46 - 49: 11.391 distance: 49 - 50: 4.800 distance: 50 - 51: 28.522 distance: 50 - 53: 8.975 distance: 51 - 52: 11.216 distance: 51 - 54: 11.705 distance: 54 - 55: 24.085 distance: 55 - 56: 8.242 distance: 55 - 58: 21.114 distance: 56 - 57: 19.935 distance: 56 - 59: 18.587 distance: 59 - 60: 21.043 distance: 60 - 61: 4.267 distance: 60 - 63: 8.780 distance: 61 - 62: 20.057 distance: 61 - 64: 8.161 distance: 64 - 65: 3.371 distance: 65 - 66: 16.628 distance: 65 - 68: 13.526 distance: 66 - 67: 13.685 distance: 66 - 69: 7.965 distance: 69 - 70: 9.731 distance: 70 - 71: 3.588 distance: 70 - 73: 17.458 distance: 71 - 74: 9.340