Starting phenix.real_space_refine on Sat Jan 25 22:46:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7utz_26795/01_2025/7utz_26795_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7utz_26795/01_2025/7utz_26795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7utz_26795/01_2025/7utz_26795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7utz_26795/01_2025/7utz_26795.map" model { file = "/net/cci-nas-00/data/ceres_data/7utz_26795/01_2025/7utz_26795_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7utz_26795/01_2025/7utz_26795_trim.cif" } resolution = 2.4 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= 0.026 sd= 0.080 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 S 100 5.16 5 C 7680 2.51 5 N 2039 2.21 5 O 2228 1.98 5 H 11632 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 23679 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1273 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1648 Classifications: {'peptide': 109} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "N" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1893 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "R" Number of atoms: 9460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 9460 Classifications: {'peptide': 600} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 572} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "X" Number of atoms: 3286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3286 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 102 Chain: "Y" Number of atoms: 5110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5110 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "Z" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 871 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Unusual residues: {'NAG': 4, 'Z41': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 12.09, per 1000 atoms: 0.51 Number of scatterers: 23679 At special positions: 0 Unit cell: (177.834, 133.791, 108.03, 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) S 100 16.00 O 2228 8.00 N 2039 7.00 C 7680 6.00 H 11632 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 31 " distance=2.03 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 82 " distance=2.03 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 2 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 67 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 83 " distance=2.03 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS B 85 " distance=2.03 Simple disulfide: pdb=" SG CYS B 88 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS R 24 " - pdb=" SG CYS R 31 " distance=2.03 Simple disulfide: pdb=" SG CYS R 29 " - pdb=" SG CYS R 41 " distance=2.03 Simple disulfide: pdb=" SG CYS R 283 " - pdb=" SG CYS R 398 " distance=2.03 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 408 " distance=2.03 Simple disulfide: pdb=" SG CYS R 301 " - pdb=" SG CYS R 390 " distance=2.03 Simple disulfide: pdb=" SG CYS R 494 " - pdb=" SG CYS R 569 " 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 Links applied NAG-ASN " NAG A 101 " - " ASN A 78 " " NAG A 102 " - " ASN A 52 " " NAG B 201 " - " ASN B 23 " " NAG R 801 " - " ASN R 99 " " NAG R 802 " - " ASN R 77 " " NAG R 803 " - " ASN R 198 " " NAG R 804 " - " ASN R 177 " Time building additional restraints: 6.46 Conformation dependent library (CDL) restraints added in 2.1 seconds 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 19 sheets defined 32.7% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'B' and resid 43 through 48 removed outlier: 3.697A pdb=" N SER B 48 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.633A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 172 through 176 removed outlier: 3.777A pdb=" N LEU R 175 " --> pdb=" O PHE R 172 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N CYS R 176 " --> pdb=" O GLN R 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 172 through 176' Processing helix chain 'R' and resid 218 through 222 removed outlier: 4.387A pdb=" N PHE R 221 " --> pdb=" O LYS R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 287 removed outlier: 3.521A pdb=" N LYS R 287 " --> pdb=" O CYS R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 305 removed outlier: 3.856A pdb=" N SER R 305 " --> pdb=" O CYS R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 391 Processing helix chain 'R' and resid 416 through 442 removed outlier: 4.683A pdb=" N TRP R 422 " --> pdb=" O ARG R 418 " (cutoff:3.500A) Processing helix chain 'R' and resid 447 through 477 Processing helix chain 'R' and resid 480 through 491 removed outlier: 3.715A pdb=" N HIS R 484 " --> pdb=" O GLU R 480 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ILE R 486 " --> pdb=" O TYR R 482 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ASP R 487 " --> pdb=" O ASN R 483 " (cutoff:3.500A) Processing helix chain 'R' and resid 491 through 525 removed outlier: 4.068A pdb=" N ASN R 495 " --> pdb=" O GLY R 491 " (cutoff:3.500A) Processing helix chain 'R' and resid 528 through 532 Processing helix chain 'R' and resid 534 through 559 Proline residue: R 556 - end of helix Processing helix chain 'R' and resid 576 through 609 Processing helix chain 'R' and resid 620 through 649 removed outlier: 3.895A pdb=" N LEU R 629 " --> pdb=" O ARG R 625 " (cutoff:3.500A) Proline residue: R 639 - end of helix Processing helix chain 'R' and resid 655 through 666 removed outlier: 3.725A pdb=" N LYS R 660 " --> pdb=" O VAL R 656 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE R 661 " --> pdb=" O SER R 657 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU R 662 " --> pdb=" O ASN R 658 " (cutoff:3.500A) Processing helix chain 'R' and resid 668 through 679 Proline residue: R 675 - end of helix Processing helix chain 'R' and resid 682 through 697 Processing helix chain 'X' and resid 15 through 40 Processing helix chain 'X' and resid 52 through 59 Processing helix chain 'X' and resid 233 through 239 removed outlier: 3.516A pdb=" N ASN X 239 " --> pdb=" O GLN X 236 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 279 Processing helix chain 'X' and resid 293 through 304 removed outlier: 3.571A pdb=" N GLY X 304 " --> pdb=" O LYS X 300 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 317 Processing helix chain 'X' and resid 331 through 352 removed outlier: 4.015A pdb=" N THR X 335 " --> pdb=" O ASP X 331 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE X 345 " --> pdb=" O ILE X 341 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER X 352 " --> pdb=" O ILE X 348 " (cutoff:3.500A) Processing helix chain 'X' and resid 370 through 391 Processing helix chain 'Y' and resid 4 through 25 Processing helix chain 'Y' and resid 29 through 34 Processing helix chain 'Z' and resid 8 through 24 Processing helix chain 'Z' and resid 29 through 45 Processing helix chain 'Z' and resid 46 through 48 No H-bonds generated for 'chain 'Z' and resid 46 through 48' Processing helix chain 'Z' and resid 55 through 59 removed outlier: 3.639A pdb=" N GLU Z 58 " --> pdb=" O PRO Z 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 11 removed outlier: 3.510A pdb=" N LEU B 20 " --> pdb=" O ILE B 11 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N THR B 25 " --> pdb=" O PRO A 38 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N CYS B 31 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS A 32 " --> pdb=" O CYS B 31 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL A 53 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE B 96 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N SER A 55 " --> pdb=" O ILE B 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 69 removed outlier: 6.432A pdb=" N ALA A 81 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR A 65 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N HIS A 79 " --> pdb=" O TYR A 65 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG A 67 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU A 77 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR A 69 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS A 75 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 63 removed outlier: 6.892A pdb=" N SER B 82 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE B 57 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ALA B 80 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR B 59 " --> pdb=" O PRO B 78 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR B 61 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER B 76 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLU B 63 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N TYR B 74 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.531A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.533A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN N 39 " --> pdb=" O VAL N 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 30 through 33 removed outlier: 3.668A pdb=" N ARG R 38 " --> pdb=" O HIS R 32 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU R 57 " --> pdb=" O TYR R 82 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N SER R 84 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU R 59 " --> pdb=" O SER R 84 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE R 81 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ARG R 109 " --> pdb=" O ILE R 81 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL R 83 " --> pdb=" O ARG R 109 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR R 111 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE R 106 " --> pdb=" O GLY R 132 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE R 134 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE R 108 " --> pdb=" O PHE R 134 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR R 136 " --> pdb=" O ILE R 108 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASN R 110 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU R 131 " --> pdb=" O GLU R 157 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N THR R 159 " --> pdb=" O LEU R 131 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE R 133 " --> pdb=" O THR R 159 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE R 154 " --> pdb=" O THR R 181 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LYS R 183 " --> pdb=" O PHE R 154 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU R 156 " --> pdb=" O LYS R 183 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU R 180 " --> pdb=" O LEU R 202 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA R 204 " --> pdb=" O LEU R 180 " (cutoff:3.500A) removed outlier: 9.809A pdb=" N LEU R 230 " --> pdb=" O LYS R 201 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP R 203 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N ASP R 232 " --> pdb=" O ASP R 203 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL R 205 " --> pdb=" O ASP R 232 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU R 231 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU R 252 " --> pdb=" O ASP R 276 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA R 275 " --> pdb=" O THR R 399 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 66 through 67 Processing sheet with id=AB1, first strand: chain 'R' and resid 97 through 98 removed outlier: 6.231A pdb=" N PHE R 97 " --> pdb=" O LYS R 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'R' and resid 166 through 167 Processing sheet with id=AB3, first strand: chain 'X' and resid 210 through 214 removed outlier: 7.201A pdb=" N ARG X 42 " --> pdb=" O ALA X 243 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE X 245 " --> pdb=" O ARG X 42 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU X 44 " --> pdb=" O ILE X 245 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL X 247 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU X 46 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ASP X 249 " --> pdb=" O LEU X 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 46 through 51 removed outlier: 6.554A pdb=" N ILE Y 338 " --> pdb=" O ARG Y 48 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR Y 50 " --> pdb=" O LEU Y 336 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU Y 336 " --> pdb=" O THR Y 50 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS Y 317 " --> pdb=" O GLY Y 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 58 through 63 removed outlier: 3.707A pdb=" N ALA Y 60 " --> pdb=" O ALA Y 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU Y 70 " --> pdb=" O TRP Y 82 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS Y 78 " --> pdb=" O SER Y 74 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP Y 83 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS Y 89 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Y' and resid 100 through 105 removed outlier: 6.733A pdb=" N GLY Y 115 " --> pdb=" O MET Y 101 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N CYS Y 103 " --> pdb=" O ALA Y 113 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA Y 113 " --> pdb=" O CYS Y 103 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TYR Y 105 " --> pdb=" O TYR Y 111 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N TYR Y 111 " --> pdb=" O TYR Y 105 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE Y 123 " --> pdb=" O SER Y 136 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG Y 134 " --> pdb=" O ASN Y 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Y' and resid 146 through 151 removed outlier: 3.571A pdb=" N CYS Y 148 " --> pdb=" O SER Y 160 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP Y 170 " --> pdb=" O GLN Y 176 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLN Y 176 " --> pdb=" O ASP Y 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Y' and resid 187 through 192 removed outlier: 7.086A pdb=" N GLY Y 202 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU Y 190 " --> pdb=" O VAL Y 200 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL Y 200 " --> pdb=" O LEU Y 190 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU Y 192 " --> pdb=" O LEU Y 198 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU Y 198 " --> pdb=" O LEU Y 192 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA Y 208 " --> pdb=" O THR Y 221 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N THR Y 221 " --> pdb=" O ALA Y 208 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU Y 210 " --> pdb=" O ARG Y 219 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Y' and resid 233 through 234 removed outlier: 6.623A pdb=" N CYS Y 250 " --> pdb=" O THR Y 263 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR Y 263 " --> pdb=" O CYS Y 250 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU Y 252 " --> pdb=" O LEU Y 261 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN Y 259 " --> pdb=" O ASP Y 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 273 through 278 removed outlier: 6.417A pdb=" N CYS Y 294 " --> pdb=" O VAL Y 307 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL Y 307 " --> pdb=" O CYS Y 294 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL Y 296 " --> pdb=" O ALA Y 305 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.18 Time building geometry restraints manager: 7.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11598 1.04 - 1.23: 822 1.23 - 1.43: 4503 1.43 - 1.63: 6882 1.63 - 1.83: 132 Bond restraints: 23937 Sorted by residual: bond pdb=" N GLY X 304 " pdb=" CA GLY X 304 " ideal model delta sigma weight residual 1.448 1.494 -0.045 1.43e-02 4.89e+03 1.00e+01 bond pdb=" N GLY R 21 " pdb=" CA GLY R 21 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.96e+00 bond pdb=" C ALA X 303 " pdb=" N GLY X 304 " ideal model delta sigma weight residual 1.331 1.359 -0.028 1.32e-02 5.74e+03 4.44e+00 bond pdb=" N GLY X 353 " pdb=" CA GLY X 353 " ideal model delta sigma weight residual 1.449 1.477 -0.027 1.45e-02 4.76e+03 3.56e+00 bond pdb=" C ALA B 72 " pdb=" N PRO B 73 " ideal model delta sigma weight residual 1.336 1.353 -0.018 9.80e-03 1.04e+04 3.21e+00 ... (remaining 23932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 42360 2.06 - 4.12: 578 4.12 - 6.18: 73 6.18 - 8.24: 4 8.24 - 10.30: 1 Bond angle restraints: 43016 Sorted by residual: angle pdb=" N SER R 26 " pdb=" CA SER R 26 " pdb=" C SER R 26 " ideal model delta sigma weight residual 108.13 111.50 -3.37 9.00e-01 1.23e+00 1.40e+01 angle pdb=" C30 Z41 R 805 " pdb=" C31 Z41 R 805 " pdb=" C32 Z41 R 805 " ideal model delta sigma weight residual 114.63 104.33 10.30 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C ALA X 303 " pdb=" N GLY X 304 " pdb=" CA GLY X 304 " ideal model delta sigma weight residual 121.07 126.56 -5.49 1.79e+00 3.12e-01 9.40e+00 angle pdb=" C PRO N 102 " pdb=" N PHE N 103 " pdb=" CA PHE N 103 " ideal model delta sigma weight residual 121.70 126.96 -5.26 1.80e+00 3.09e-01 8.55e+00 angle pdb=" CA TRP X 234 " pdb=" CB TRP X 234 " pdb=" CG TRP X 234 " ideal model delta sigma weight residual 113.60 119.05 -5.45 1.90e+00 2.77e-01 8.21e+00 ... (remaining 43011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10456 17.94 - 35.88: 812 35.88 - 53.82: 208 53.82 - 71.76: 50 71.76 - 89.70: 22 Dihedral angle restraints: 11548 sinusoidal: 6188 harmonic: 5360 Sorted by residual: dihedral pdb=" CB CYS R 494 " pdb=" SG CYS R 494 " pdb=" SG CYS R 569 " pdb=" CB CYS R 569 " ideal model delta sinusoidal sigma weight residual -86.00 -35.35 -50.65 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS R 301 " pdb=" SG CYS R 301 " pdb=" SG CYS R 390 " pdb=" CB CYS R 390 " ideal model delta sinusoidal sigma weight residual -86.00 -134.08 48.08 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CA SER X 352 " pdb=" C SER X 352 " pdb=" N GLY X 353 " pdb=" CA GLY X 353 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 11545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1476 0.047 - 0.093: 349 0.093 - 0.140: 104 0.140 - 0.187: 6 0.187 - 0.233: 1 Chirality restraints: 1936 Sorted by residual: chirality pdb=" CA GLU X 27 " pdb=" N GLU X 27 " pdb=" C GLU X 27 " pdb=" CB GLU X 27 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA CYS A 7 " pdb=" N CYS A 7 " pdb=" C CYS A 7 " pdb=" CB CYS A 7 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA ILE R 47 " pdb=" N ILE R 47 " pdb=" C ILE R 47 " pdb=" CB ILE R 47 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 1933 not shown) Planarity restraints: 3579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER X 352 " 0.035 2.00e-02 2.50e+03 6.98e-02 4.87e+01 pdb=" C SER X 352 " -0.121 2.00e-02 2.50e+03 pdb=" O SER X 352 " 0.046 2.00e-02 2.50e+03 pdb=" N GLY X 353 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA X 303 " 0.034 2.00e-02 2.50e+03 6.78e-02 4.60e+01 pdb=" C ALA X 303 " -0.117 2.00e-02 2.50e+03 pdb=" O ALA X 303 " 0.044 2.00e-02 2.50e+03 pdb=" N GLY X 304 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER X 352 " 0.016 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" N GLY X 353 " -0.050 2.00e-02 2.50e+03 pdb=" CA GLY X 353 " 0.013 2.00e-02 2.50e+03 pdb=" H GLY X 353 " 0.022 2.00e-02 2.50e+03 ... (remaining 3576 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 3345 2.27 - 2.85: 53434 2.85 - 3.44: 62469 3.44 - 4.02: 87418 4.02 - 4.60: 131738 Nonbonded interactions: 338404 Sorted by model distance: nonbonded pdb=" O LEU X 44 " pdb=" H ILE X 245 " model vdw 1.689 2.450 nonbonded pdb="HD21 ASN X 23 " pdb=" OE1 GLU X 27 " model vdw 1.704 2.450 nonbonded pdb="HD22 ASN Y 230 " pdb=" OD1 ASP Y 246 " model vdw 1.716 2.450 nonbonded pdb=" O ALA R 254 " pdb=" HG SER R 278 " model vdw 1.720 2.450 nonbonded pdb=" OD1 ASP R 160 " pdb="HD21 ASN R 186 " model vdw 1.723 2.450 ... (remaining 338399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.670 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: 0.420 Extract box with map and model: 0.960 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 52.040 Find NCS groups from input model: 0.180 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:11.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 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 0.045 12305 Z= 0.264 Angle : 0.694 10.300 16698 Z= 0.361 Chirality : 0.044 0.233 1936 Planarity : 0.005 0.077 2104 Dihedral : 12.457 81.074 4519 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.08 % Allowed : 0.31 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.07 % 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: -0.05 (0.21), residues: 1514 helix: 1.63 (0.25), residues: 431 sheet: -1.13 (0.28), residues: 322 loop : -0.43 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 234 HIS 0.005 0.001 HIS Y 311 PHE 0.018 0.001 PHE Y 235 TYR 0.015 0.001 TYR R 667 ARG 0.016 0.001 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8204 (t) cc_final: 0.7897 (m) REVERT: B 50 ASP cc_start: 0.5881 (p0) cc_final: 0.5378 (p0) REVERT: N 28 THR cc_start: 0.8411 (t) cc_final: 0.8019 (m) REVERT: N 114 THR cc_start: 0.8070 (p) cc_final: 0.7845 (t) REVERT: R 45 GLN cc_start: 0.7136 (mm-40) cc_final: 0.6376 (tp-100) REVERT: R 98 TYR cc_start: 0.6942 (t80) cc_final: 0.6666 (t80) REVERT: R 274 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7280 (mtp85) REVERT: R 437 LEU cc_start: 0.7303 (pp) cc_final: 0.6912 (mt) REVERT: R 688 ASP cc_start: 0.6794 (m-30) cc_final: 0.6480 (m-30) REVERT: Y 35 ASN cc_start: 0.6518 (m-40) cc_final: 0.6152 (m110) REVERT: Y 110 ASN cc_start: 0.6764 (m-40) cc_final: 0.6376 (t0) REVERT: Y 259 GLN cc_start: 0.6891 (tt0) cc_final: 0.6493 (pt0) REVERT: Y 334 SER cc_start: 0.7907 (p) cc_final: 0.7668 (m) REVERT: Z 46 LYS cc_start: 0.7841 (mppt) cc_final: 0.7004 (pttm) REVERT: Z 47 GLU cc_start: 0.6925 (pm20) cc_final: 0.6221 (pp20) outliers start: 1 outliers final: 1 residues processed: 244 average time/residue: 2.5640 time to fit residues: 683.6450 Evaluate side-chains 159 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 125 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.0370 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN N 35 ASN N 120 GLN Z 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.136913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.120966 restraints weight = 59544.420| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.71 r_work: 0.3885 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12305 Z= 0.343 Angle : 0.614 6.573 16698 Z= 0.333 Chirality : 0.044 0.322 1936 Planarity : 0.005 0.058 2104 Dihedral : 7.226 62.276 1857 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.40 % Allowed : 9.88 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1514 helix: 1.86 (0.25), residues: 424 sheet: -1.32 (0.27), residues: 344 loop : -0.47 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Y 82 HIS 0.006 0.001 HIS A 83 PHE 0.026 0.002 PHE R 500 TYR 0.015 0.002 TYR Y 264 ARG 0.010 0.001 ARG X 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.6701 (p0) cc_final: 0.6221 (p0) REVERT: N 3 GLN cc_start: 0.7199 (tm-30) cc_final: 0.6967 (tm-30) REVERT: N 28 THR cc_start: 0.8916 (t) cc_final: 0.8551 (m) REVERT: R 38 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7437 (mtp85) REVERT: R 45 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6890 (mm-40) REVERT: R 286 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: R 396 MET cc_start: 0.8025 (tmt) cc_final: 0.7517 (tmt) REVERT: R 437 LEU cc_start: 0.7428 (pp) cc_final: 0.6949 (mt) REVERT: R 609 ARG cc_start: 0.5677 (ttt-90) cc_final: 0.5393 (tpt-90) REVERT: R 688 ASP cc_start: 0.6989 (m-30) cc_final: 0.6639 (m-30) REVERT: Y 35 ASN cc_start: 0.6781 (m-40) cc_final: 0.6367 (m110) REVERT: Y 46 ARG cc_start: 0.6608 (mmm160) cc_final: 0.6159 (mmm160) REVERT: Y 72 SER cc_start: 0.8163 (t) cc_final: 0.7941 (m) REVERT: Y 110 ASN cc_start: 0.7299 (m-40) cc_final: 0.6952 (t0) REVERT: Y 215 GLU cc_start: 0.7093 (pm20) cc_final: 0.6866 (pm20) REVERT: Z 46 LYS cc_start: 0.7863 (mppt) cc_final: 0.7132 (pttm) REVERT: Z 47 GLU cc_start: 0.7170 (pm20) cc_final: 0.6363 (pp20) outliers start: 18 outliers final: 9 residues processed: 193 average time/residue: 2.6949 time to fit residues: 567.6273 Evaluate side-chains 177 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 38 ARG Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 283 CYS Chi-restraints excluded: chain R residue 286 PHE Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain R residue 487 ASP Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain Y residue 98 SER Chi-restraints excluded: chain Y residue 112 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 69.8167 > 50: distance: 90 - 342: 23.363 distance: 178 - 182: 3.173 distance: 186 - 242: 19.285 distance: 193 - 237: 28.435 distance: 199 - 247: 34.593 distance: 223 - 237: 27.774 distance: 237 - 238: 16.323 distance: 237 - 243: 7.205 distance: 238 - 239: 35.552 distance: 238 - 241: 25.426 distance: 238 - 244: 16.622 distance: 239 - 240: 18.642 distance: 239 - 247: 7.058 distance: 241 - 242: 29.507 distance: 241 - 245: 13.151 distance: 247 - 248: 40.019 distance: 248 - 249: 39.659 distance: 248 - 252: 41.399 distance: 248 - 253: 53.526 distance: 249 - 250: 29.320 distance: 249 - 254: 43.473 distance: 254 - 255: 17.568 distance: 254 - 262: 28.704 distance: 255 - 256: 15.495 distance: 255 - 258: 13.572 distance: 255 - 263: 30.353 distance: 256 - 257: 20.122 distance: 256 - 266: 26.293 distance: 258 - 259: 13.423 distance: 258 - 264: 26.372 distance: 258 - 265: 21.891 distance: 259 - 260: 16.567 distance: 259 - 261: 17.781 distance: 266 - 267: 19.714 distance: 266 - 272: 19.024 distance: 267 - 268: 16.272 distance: 267 - 270: 11.309 distance: 267 - 273: 30.173 distance: 268 - 269: 12.377 distance: 268 - 277: 15.349 distance: 270 - 274: 3.350 distance: 270 - 275: 13.466 distance: 271 - 276: 19.608 distance: 277 - 278: 16.756 distance: 277 - 286: 5.071 distance: 278 - 279: 43.693 distance: 278 - 281: 23.578 distance: 278 - 287: 7.874 distance: 279 - 292: 13.009 distance: 281 - 282: 19.482 distance: 281 - 288: 7.465 distance: 282 - 283: 10.934 distance: 282 - 290: 14.526 distance: 282 - 291: 13.337 distance: 283 - 284: 16.943 distance: 283 - 285: 21.395 distance: 292 - 300: 10.105 distance: 293 - 294: 51.949 distance: 293 - 296: 40.187 distance: 294 - 295: 7.286 distance: 294 - 304: 38.219 distance: 296 - 297: 3.527 distance: 296 - 303: 8.363 distance: 297 - 298: 8.783 distance: 297 - 299: 13.865 distance: 304 - 305: 9.428 distance: 304 - 312: 13.810 distance: 305 - 306: 28.298 distance: 305 - 308: 16.248 distance: 305 - 313: 13.225 distance: 306 - 307: 33.512 distance: 306 - 321: 41.744 distance: 308 - 309: 14.206 distance: 308 - 314: 9.208 distance: 308 - 315: 17.688 distance: 309 - 310: 22.636 distance: 309 - 316: 7.747 distance: 309 - 317: 10.541 distance: 310 - 311: 15.270 distance: 311 - 318: 3.652 distance: 311 - 319: 6.281 distance: 321 - 328: 17.843 distance: 322 - 323: 42.032 distance: 322 - 325: 26.626 distance: 322 - 329: 14.498 distance: 323 - 324: 18.263 distance: 323 - 337: 46.528 distance: 325 - 326: 39.596 distance: 325 - 327: 15.374 distance: 325 - 330: 18.440 distance: 326 - 331: 4.224 distance: 326 - 332: 14.726 distance: 326 - 333: 15.388 distance: 327 - 334: 11.536 distance: 327 - 335: 6.864 distance: 327 - 336: 4.839 distance: 337 - 338: 35.921 distance: 337 - 343: 17.294 distance: 338 - 339: 44.660 distance: 338 - 341: 15.968 distance: 338 - 344: 19.374 distance: 339 - 340: 30.248 distance: 339 - 347: 40.372 distance: 341 - 342: 30.131 distance: 341 - 345: 19.311 distance: 341 - 346: 22.376 distance: 347 - 348: 67.504 distance: 347 - 354: 56.724 distance: 348 - 349: 3.075 distance: 348 - 351: 33.219 distance: 348 - 355: 36.802 distance: 349 - 361: 35.089 distance: 351 - 352: 17.562 distance: 351 - 353: 18.236 distance: 351 - 356: 29.215 distance: 352 - 357: 40.803 distance: 353 - 358: 29.256 distance: 353 - 359: 7.633 distance: 353 - 360: 11.312