Starting phenix.real_space_refine on Thu May 15 18:55:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tao_41139/05_2025/8tao_41139.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tao_41139/05_2025/8tao_41139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tao_41139/05_2025/8tao_41139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tao_41139/05_2025/8tao_41139.map" model { file = "/net/cci-nas-00/data/ceres_data/8tao_41139/05_2025/8tao_41139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tao_41139/05_2025/8tao_41139.cif" } resolution = 2.9 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 150 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 8509 2.51 5 N 2286 2.21 5 O 2514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13422 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 5804 Classifications: {'peptide': 777} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 744} Chain breaks: 2 Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 415 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 171 Chain: "B" Number of atoms: 5694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5694 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 738} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 408 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 337 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 9, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 228 Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 939 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "D" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 931 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'QUS': 1, 'YKU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.99, per 1000 atoms: 0.67 Number of scatterers: 13422 At special positions: 0 Unit cell: (109.989, 85.547, 208.868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 2514 8.00 N 2286 7.00 C 8509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 98 " distance=2.04 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: 3.68 Conformation dependent library (CDL) restraints added in 1.9 seconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3326 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 21 sheets defined 43.8% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 66 through 81 removed outlier: 3.629A pdb=" N GLU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 121 removed outlier: 4.491A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N SER A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.707A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.700A pdb=" N LEU A 179 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER A 180 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP A 181 " --> pdb=" O ASP A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 181' Processing helix chain 'A' and resid 195 through 209 removed outlier: 3.502A pdb=" N TYR A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 239 Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.548A pdb=" N PHE A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.731A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 396 through 419 removed outlier: 3.907A pdb=" N MET A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.727A pdb=" N LYS A 430 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 577 through 603 removed outlier: 3.585A pdb=" N ALA A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.841A pdb=" N SER A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 636 removed outlier: 3.964A pdb=" N CYS A 618 " --> pdb=" O SER A 614 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 672 removed outlier: 3.718A pdb=" N LEU A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 648 " --> pdb=" O CYS A 644 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE A 649 " --> pdb=" O TYR A 645 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 654 " --> pdb=" O GLY A 650 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 3.717A pdb=" N ALA A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE A 672 " --> pdb=" O ARG A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 715 removed outlier: 3.711A pdb=" N VAL A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 761 Proline residue: A 743 - end of helix Processing helix chain 'A' and resid 774 through 795 Proline residue: A 790 - end of helix removed outlier: 4.312A pdb=" N PHE A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY A 794 " --> pdb=" O PRO A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 826 Proline residue: A 820 - end of helix Processing helix chain 'B' and resid 65 through 81 removed outlier: 3.976A pdb=" N VAL B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 120 removed outlier: 4.635A pdb=" N ASP B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 164 removed outlier: 4.272A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 181 removed outlier: 3.641A pdb=" N LEU B 179 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 180 " --> pdb=" O MET B 177 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP B 181 " --> pdb=" O ASP B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 181' Processing helix chain 'B' and resid 195 through 209 Processing helix chain 'B' and resid 221 through 236 Processing helix chain 'B' and resid 253 through 267 removed outlier: 3.666A pdb=" N LYS B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 260 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 261 " --> pdb=" O PHE B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 294 Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.713A pdb=" N ALA B 308 " --> pdb=" O ASP B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.978A pdb=" N VAL B 322 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 342 removed outlier: 4.098A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 340 " --> pdb=" O TRP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 removed outlier: 3.781A pdb=" N GLN B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN B 360 " --> pdb=" O GLN B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 419 removed outlier: 3.583A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.526A pdb=" N LYS B 430 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 443 removed outlier: 3.896A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 604 removed outlier: 3.594A pdb=" N ILE B 581 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 583 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B 590 " --> pdb=" O PHE B 586 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 601 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 614 through 637 removed outlier: 3.596A pdb=" N CYS B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 673 removed outlier: 3.868A pdb=" N GLY B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) Proline residue: B 655 - end of helix removed outlier: 3.523A pdb=" N LEU B 662 " --> pdb=" O SER B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 715 removed outlier: 3.516A pdb=" N GLN B 693 " --> pdb=" O SER B 689 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 762 removed outlier: 3.514A pdb=" N VAL B 740 " --> pdb=" O THR B 736 " (cutoff:3.500A) Proline residue: B 743 - end of helix removed outlier: 3.634A pdb=" N ASN B 747 " --> pdb=" O PRO B 743 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 748 " --> pdb=" O LEU B 744 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 749 " --> pdb=" O GLY B 745 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 750 " --> pdb=" O TYR B 746 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 759 " --> pdb=" O THR B 755 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 795 removed outlier: 3.979A pdb=" N ALA B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Proline residue: B 790 - end of helix removed outlier: 3.553A pdb=" N PHE B 793 " --> pdb=" O VAL B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 817 removed outlier: 4.022A pdb=" N MET B 817 " --> pdb=" O ALA B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 826 Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.897A pdb=" N THR C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.761A pdb=" N THR D 93 " --> pdb=" O PRO D 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.130A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLU A 94 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE A 36 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY A 145 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 248 removed outlier: 6.319A pdb=" N VAL A 214 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N HIS A 244 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR A 213 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ALA A 275 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER A 215 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N PHE A 277 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL A 217 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 274 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 329 removed outlier: 6.916A pdb=" N TYR A 466 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER A 486 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 468 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 523 Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 545 removed outlier: 3.868A pdb=" N PHE A 544 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 558 Processing sheet with id=AA8, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.296A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE B 36 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY B 145 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 241 through 248 removed outlier: 8.109A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS B 218 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TYR B 213 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ALA B 275 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER B 215 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N PHE B 277 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 217 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL B 274 " --> pdb=" O LEU B 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 329 removed outlier: 7.066A pdb=" N TYR B 466 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N SER B 486 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 468 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 445 through 447 Processing sheet with id=AB4, first strand: chain 'B' and resid 520 through 523 Processing sheet with id=AB5, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AB6, first strand: chain 'B' and resid 719 through 722 Processing sheet with id=AB7, first strand: chain 'C' and resid 6 through 9 Processing sheet with id=AB8, first strand: chain 'C' and resid 13 through 15 removed outlier: 6.651A pdb=" N VAL C 14 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG C 40 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N SER C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 13 through 15 removed outlier: 6.651A pdb=" N VAL C 14 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N CYS C 98 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TRP C 115 " --> pdb=" O CYS C 98 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA C 100 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 5 through 9 Processing sheet with id=AC2, first strand: chain 'D' and resid 12 through 15 removed outlier: 3.837A pdb=" N ALA D 51 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG D 40 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N SER D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 12 through 15 removed outlier: 3.592A pdb=" N TYR D 114 " --> pdb=" O ALA D 100 " (cutoff:3.500A) 659 hydrogen bonds defined for protein. 1875 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: 4.59 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2207 1.27 - 1.41: 3455 1.41 - 1.54: 7861 1.54 - 1.68: 35 1.68 - 1.82: 163 Bond restraints: 13721 Sorted by residual: bond pdb=" C19 YKU B 901 " pdb=" C21 YKU B 901 " ideal model delta sigma weight residual 1.429 1.527 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C13 YKU B 901 " pdb=" N12 YKU B 901 " ideal model delta sigma weight residual 1.359 1.453 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C05 QUS A 901 " pdb=" N15 QUS A 901 " ideal model delta sigma weight residual 1.365 1.440 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C05 QUS B 902 " pdb=" N15 QUS B 902 " ideal model delta sigma weight residual 1.365 1.440 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C04 YKU B 901 " pdb=" C07 YKU B 901 " ideal model delta sigma weight residual 1.465 1.529 -0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 13716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 18541 2.71 - 5.43: 97 5.43 - 8.14: 13 8.14 - 10.85: 1 10.85 - 13.57: 2 Bond angle restraints: 18654 Sorted by residual: angle pdb=" C03 QUS B 902 " pdb=" N14 QUS B 902 " pdb=" O20 QUS B 902 " ideal model delta sigma weight residual 112.77 126.34 -13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C03 QUS A 901 " pdb=" N14 QUS A 901 " pdb=" O20 QUS A 901 " ideal model delta sigma weight residual 112.77 126.19 -13.42 3.00e+00 1.11e-01 2.00e+01 angle pdb=" CA LEU B 567 " pdb=" CB LEU B 567 " pdb=" CG LEU B 567 " ideal model delta sigma weight residual 116.30 126.22 -9.92 3.50e+00 8.16e-02 8.04e+00 angle pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" N ASN A 222 " ideal model delta sigma weight residual 114.23 116.54 -2.31 8.80e-01 1.29e+00 6.91e+00 angle pdb=" O16 QUS A 901 " pdb=" C01 QUS A 901 " pdb=" O17 QUS A 901 " ideal model delta sigma weight residual 127.01 119.59 7.42 3.00e+00 1.11e-01 6.11e+00 ... (remaining 18649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 7404 17.78 - 35.57: 613 35.57 - 53.35: 125 53.35 - 71.14: 14 71.14 - 88.92: 10 Dihedral angle restraints: 8166 sinusoidal: 2975 harmonic: 5191 Sorted by residual: dihedral pdb=" CB CYS B 537 " pdb=" SG CYS B 537 " pdb=" SG CYS B 549 " pdb=" CB CYS B 549 " ideal model delta sinusoidal sigma weight residual 93.00 162.29 -69.29 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CB CYS B 515 " pdb=" SG CYS B 515 " pdb=" SG CYS B 534 " pdb=" CB CYS B 534 " ideal model delta sinusoidal sigma weight residual -86.00 -140.14 54.14 1 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" CB CYS A 515 " pdb=" SG CYS A 515 " pdb=" SG CYS A 534 " pdb=" CB CYS A 534 " ideal model delta sinusoidal sigma weight residual -86.00 -123.82 37.82 1 1.00e+01 1.00e-02 2.02e+01 ... (remaining 8163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1368 0.034 - 0.069: 528 0.069 - 0.103: 131 0.103 - 0.137: 61 0.137 - 0.172: 3 Chirality restraints: 2091 Sorted by residual: chirality pdb=" CA ILE A 520 " pdb=" N ILE A 520 " pdb=" C ILE A 520 " pdb=" CB ILE A 520 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA ILE A 774 " pdb=" N ILE A 774 " pdb=" C ILE A 774 " pdb=" CB ILE A 774 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA VAL A 819 " pdb=" N VAL A 819 " pdb=" C VAL A 819 " pdb=" CB VAL A 819 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 2088 not shown) Planarity restraints: 2395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 89 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO C 90 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 410 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.73e+00 pdb=" C GLY A 410 " -0.023 2.00e-02 2.50e+03 pdb=" O GLY A 410 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU A 411 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP C 107 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO C 108 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 108 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 108 " -0.015 5.00e-02 4.00e+02 ... (remaining 2392 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2268 2.76 - 3.30: 12596 3.30 - 3.83: 21465 3.83 - 4.37: 24802 4.37 - 4.90: 43980 Nonbonded interactions: 105111 Sorted by model distance: nonbonded pdb=" OH TYR A 209 " pdb=" OD1 ASP A 496 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR B 311 " pdb=" OD1 ASP B 480 " model vdw 2.263 3.040 nonbonded pdb=" O LEU A 591 " pdb=" OG1 THR A 594 " model vdw 2.265 3.040 nonbonded pdb=" OG SER C 54 " pdb=" O GLY C 57 " model vdw 2.280 3.040 nonbonded pdb=" O GLY B 624 " pdb=" OG SER B 654 " model vdw 2.280 3.040 ... (remaining 105106 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 297 or (resid 298 and (name N or name CA or nam \ e C or name O or name CB )) or resid 299 through 378 or (resid 379 and (name N o \ r name CA or name C or name O or name CB )) or resid 380 through 523 or (resid 5 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 525 through \ 595 or (resid 596 and (name N or name CA or name C or name O or name CB )) or r \ esid 597 through 602 or (resid 603 and (name N or name CA or name C or name O or \ name CB )) or resid 604 through 619 or (resid 620 and (name N or name CA or nam \ e C or name O or name CB )) or resid 621 or (resid 622 through 623 and (name N o \ r name CA or name C or name O or name CB )) or (resid 624 through 627 and (name \ N or name CA or name C or name O or name CB )) or resid 628 through 632 or (resi \ d 633 and (name N or name CA or name C or name O or name CB )) or resid 634 thro \ ugh 638 or (resid 639 through 641 and (name N or name CA or name C or name O or \ name CB )) or resid 642 through 644 or (resid 645 through 646 and (name N or nam \ e CA or name C or name O or name CB )) or resid 647 through 662 or (resid 663 an \ d (name N or name CA or name C or name O or name CB )) or resid 664 or (resid 66 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 666 through \ 671 or (resid 672 through 673 and (name N or name CA or name C or name O or name \ CB )) or resid 687 through 688 or (resid 689 through 695 and (name N or name CA \ or name C or name O or name CB )) or resid 696 through 698 or (resid 699 throug \ h 700 and (name N or name CA or name C or name O or name CB )) or resid 701 thro \ ugh 707 or (resid 708 through 715 and (name N or name CA or name C or name O or \ name CB )) or resid 716 through 736 or (resid 737 through 738 and (name N or nam \ e CA or name C or name O or name CB )) or resid 739 through 741 or (resid 742 an \ d (name N or name CA or name C or name O or name CB )) or resid 743 through 750 \ or (resid 751 through 753 and (name N or name CA or name C or name O or name CB \ )) or resid 754 through 756 or (resid 757 through 760 and (name N or name CA or \ name C or name O or name CB )) or resid 761 through 768 or (resid 769 through 77 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 773 through \ 775 or (resid 776 and (name N or name CA or name C or name O or name CB )) or re \ sid 777 through 778 or (resid 779 and (name N or name CA or name C or name O or \ name CB )) or resid 780 through 782 or (resid 783 and (name N or name CA or name \ C or name O or name CB )) or resid 784 through 787 or (resid 788 and (name N or \ name CA or name C or name O or name CB )) or resid 789 through 795 or (resid 79 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 797 through \ 803 or (resid 804 and (name N or name CA or name C or name O or name CB )) or re \ sid 805 through 822 or (resid 823 through 826 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'B' and (resid 25 through 121 or (resid 140 and (name N or name CA or nam \ e C or name O or name CB )) or resid 141 through 559 or (resid 560 and (name N o \ r name CA or name C or name O or name CB )) or resid 561 through 566 or (resid 5 \ 67 and (name N or name CA or name C or name O or name CB )) or resid 568 through \ 580 or (resid 581 through 583 and (name N or name CA or name C or name O or nam \ e CB )) or resid 584 or (resid 585 and (name N or name CA or name C or name O or \ name CB )) or resid 586 through 587 or (resid 588 through 589 and (name N or na \ me CA or name C or name O or name CB )) or resid 590 through 600 or (resid 601 t \ hrough 603 and (name N or name CA or name C or name O or name CB )) or resid 604 \ through 617 or (resid 618 through 620 and (name N or name CA or name C or name \ O or name CB )) or resid 621 through 637 or (resid 638 through 641 and (name N o \ r name CA or name C or name O or name CB )) or resid 642 or (resid 643 and (name \ N or name CA or name C or name O or name CB )) or resid 644 through 650 or (res \ id 651 and (name N or name CA or name C or name O or name CB )) or resid 652 thr \ ough 653 or (resid 654 and (name N or name CA or name C or name O or name CB )) \ or resid 655 through 656 or (resid 657 through 658 and (name N or name CA or nam \ e C or name O or name CB )) or resid 659 or (resid 660 through 661 and (name N o \ r name CA or name C or name O or name CB )) or resid 662 through 666 or (resid 6 \ 67 through 673 and (name N or name CA or name C or name O or name CB )) or resid \ 687 or (resid 688 through 695 and (name N or name CA or name C or name O or nam \ e CB )) or resid 696 through 697 or (resid 698 through 700 and (name N or name C \ A or name C or name O or name CB )) or resid 701 or (resid 702 and (name N or na \ me CA or name C or name O or name CB )) or resid 703 through 721 or (resid 722 t \ hrough 723 and (name N or name CA or name C or name O or name CB )) or resid 724 \ through 743 or (resid 744 and (name N or name CA or name C or name O or name CB \ )) or resid 745 through 785 or (resid 786 through 788 and (name N or name CA or \ name C or name O or name CB )) or resid 789 through 820 or (resid 821 through 8 \ 26 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'C' and (resid 3 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 116 or (resid 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 through 125)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.800 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 33.280 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.003 0.098 13741 Z= 0.155 Angle : 0.546 13.568 18694 Z= 0.270 Chirality : 0.041 0.172 2091 Planarity : 0.003 0.041 2395 Dihedral : 13.598 88.920 4780 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.43 (0.20), residues: 1778 helix: 1.81 (0.20), residues: 696 sheet: -0.35 (0.31), residues: 272 loop : -0.84 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 211 HIS 0.002 0.000 HIS B 267 PHE 0.013 0.001 PHE A 818 TYR 0.010 0.001 TYR A 223 ARG 0.005 0.000 ARG A 465 Details of bonding type rmsd hydrogen bonds : bond 0.15888 ( 647) hydrogen bonds : angle 5.89115 ( 1875) SS BOND : bond 0.00226 ( 20) SS BOND : angle 0.58040 ( 40) covalent geometry : bond 0.00322 (13721) covalent geometry : angle 0.54608 (18654) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.540 Fit side-chains REVERT: A 524 ARG cc_start: 0.5996 (ttt180) cc_final: 0.5766 (ttt180) REVERT: A 547 TYR cc_start: 0.7161 (m-10) cc_final: 0.6935 (m-10) REVERT: B 229 GLU cc_start: 0.6041 (pt0) cc_final: 0.5757 (pt0) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 1.3249 time to fit residues: 208.5754 Evaluate side-chains 129 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 53 optimal weight: 0.0570 chunk 84 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 161 optimal weight: 5.9990 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.128962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.086893 restraints weight = 26970.970| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.77 r_work: 0.3115 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13741 Z= 0.193 Angle : 0.565 9.284 18694 Z= 0.292 Chirality : 0.043 0.139 2091 Planarity : 0.004 0.038 2395 Dihedral : 6.158 80.594 1956 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.04 % Allowed : 7.26 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.57 (0.20), residues: 1778 helix: 2.09 (0.19), residues: 714 sheet: -0.39 (0.32), residues: 266 loop : -0.95 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 211 HIS 0.005 0.001 HIS A 218 PHE 0.015 0.001 PHE A 337 TYR 0.011 0.001 TYR A 409 ARG 0.005 0.000 ARG C 106 Details of bonding type rmsd hydrogen bonds : bond 0.05406 ( 647) hydrogen bonds : angle 4.37175 ( 1875) SS BOND : bond 0.00413 ( 20) SS BOND : angle 0.63084 ( 40) covalent geometry : bond 0.00460 (13721) covalent geometry : angle 0.56507 (18654) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 1.529 Fit side-chains REVERT: A 255 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7297 (mp10) REVERT: A 521 LYS cc_start: 0.7017 (ptpp) cc_final: 0.6279 (mttt) REVERT: B 657 MET cc_start: 0.8394 (ppp) cc_final: 0.8176 (ppp) REVERT: C 120 GLN cc_start: 0.8455 (tp-100) cc_final: 0.8220 (tp-100) REVERT: D 5 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7827 (tt0) outliers start: 14 outliers final: 5 residues processed: 133 average time/residue: 1.3622 time to fit residues: 198.0064 Evaluate side-chains 134 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain D residue 5 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.0094 > 50: distance: 8 - 12: 6.401 distance: 12 - 13: 6.756 distance: 13 - 14: 7.394 distance: 13 - 16: 10.674 distance: 14 - 15: 13.549 distance: 14 - 18: 7.404 distance: 16 - 17: 17.057 distance: 18 - 19: 10.986 distance: 19 - 20: 8.578 distance: 19 - 22: 5.397 distance: 20 - 21: 23.986 distance: 20 - 27: 7.600 distance: 22 - 23: 10.674 distance: 23 - 24: 8.849 distance: 24 - 25: 18.178 distance: 24 - 26: 17.633 distance: 27 - 28: 5.256 distance: 27 - 33: 26.338 distance: 28 - 29: 7.240 distance: 28 - 31: 4.753 distance: 29 - 30: 5.790 distance: 31 - 32: 23.054 distance: 32 - 33: 6.679 distance: 34 - 35: 8.121 distance: 35 - 36: 4.100 distance: 35 - 38: 5.429 distance: 36 - 37: 6.754 distance: 36 - 40: 3.500 distance: 38 - 39: 11.828 distance: 39 - 125: 7.406 distance: 41 - 42: 5.206 distance: 41 - 44: 3.445 distance: 42 - 43: 6.453 distance: 42 - 45: 3.401 distance: 45 - 46: 3.934 distance: 46 - 47: 4.157 distance: 47 - 48: 5.423 distance: 47 - 54: 10.120 distance: 49 - 50: 12.407 distance: 50 - 51: 10.698 distance: 51 - 52: 3.034 distance: 52 - 53: 12.148 distance: 54 - 55: 8.661 distance: 55 - 56: 7.216 distance: 56 - 57: 8.156 distance: 56 - 58: 3.603 distance: 58 - 59: 3.527 distance: 59 - 60: 3.300 distance: 60 - 61: 8.468 distance: 60 - 67: 6.343 distance: 62 - 63: 4.999 distance: 63 - 64: 6.458 distance: 64 - 65: 5.736 distance: 64 - 66: 9.120 distance: 68 - 71: 4.648 distance: 71 - 72: 3.561 distance: 71 - 73: 5.845 distance: 72 - 74: 6.687 distance: 77 - 78: 5.635 distance: 77 - 84: 4.209 distance: 78 - 126: 8.589 distance: 79 - 80: 4.016 distance: 80 - 81: 6.070 distance: 82 - 83: 6.280