Starting phenix.real_space_refine on Sun Jan 19 10:59:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pz1_18034/01_2025/8pz1_18034.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pz1_18034/01_2025/8pz1_18034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pz1_18034/01_2025/8pz1_18034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pz1_18034/01_2025/8pz1_18034.map" model { file = "/net/cci-nas-00/data/ceres_data/8pz1_18034/01_2025/8pz1_18034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pz1_18034/01_2025/8pz1_18034.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 8695 2.51 5 N 2389 2.21 5 O 2720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 13849 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 6174 Classifications: {'peptide': 782} Link IDs: {'PTRANS': 29, 'TRANS': 752} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2794 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 440 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 6, 'TRANS': 54} Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1761 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 5, 'TRANS': 84} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1978 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 8.75, per 1000 atoms: 0.63 Number of scatterers: 13849 At special positions: 0 Unit cell: (154.78, 104.37, 122.83, 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 45 16.00 O 2720 8.00 N 2389 7.00 C 8695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.9 seconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3258 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 21 sheets defined 29.7% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.551A pdb=" N MET A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 67 Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.651A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 removed outlier: 4.032A pdb=" N SER A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A 144 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.519A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 233 removed outlier: 3.749A pdb=" N LEU A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.546A pdb=" N ILE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 removed outlier: 3.758A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.636A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.816A pdb=" N ASP A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.573A pdb=" N GLU A 650 " --> pdb=" O PRO A 647 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 647 through 651' Processing helix chain 'A' and resid 726 through 730 removed outlier: 3.662A pdb=" N TYR A 729 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 730 " --> pdb=" O ASP A 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 726 through 730' Processing helix chain 'B' and resid 22 through 27 removed outlier: 3.733A pdb=" N GLU B 27 " --> pdb=" O ASN B 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.953A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.632A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.744A pdb=" N TYR D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 removed outlier: 3.743A pdb=" N ALA D 90 " --> pdb=" O PRO D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.683A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 removed outlier: 3.800A pdb=" N ARG D 141 " --> pdb=" O PRO D 137 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA D 142 " --> pdb=" O GLN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 Proline residue: D 216 - end of helix removed outlier: 3.729A pdb=" N MET D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 4.137A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL D 234 " --> pdb=" O GLN D 230 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 removed outlier: 3.625A pdb=" N ILE E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 56 Processing helix chain 'F' and resid 62 through 86 removed outlier: 3.834A pdb=" N MET F 83 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.910A pdb=" N LYS F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 150 removed outlier: 3.560A pdb=" N ARG F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE F 150 " --> pdb=" O VAL F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 159 removed outlier: 4.088A pdb=" N GLU F 158 " --> pdb=" O PRO F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 189 removed outlier: 4.388A pdb=" N SER F 189 " --> pdb=" O ASN F 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 186 through 189' Processing helix chain 'F' and resid 190 through 209 removed outlier: 3.570A pdb=" N GLU F 194 " --> pdb=" O ASP F 190 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 220 removed outlier: 3.508A pdb=" N LEU F 215 " --> pdb=" O ASP F 211 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS F 219 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 240 through 250 removed outlier: 4.695A pdb=" N GLN F 245 " --> pdb=" O GLY F 241 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALA F 246 " --> pdb=" O ILE F 242 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 249 " --> pdb=" O GLN F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 420 removed outlier: 3.823A pdb=" N ARG F 404 " --> pdb=" O MET F 400 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.298A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 98 removed outlier: 6.318A pdb=" N VAL A 163 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 96 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 5.900A pdb=" N ILE A 254 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 256 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 260 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 271 removed outlier: 7.462A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 271 removed outlier: 7.462A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 355 removed outlier: 4.336A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 425 through 427 removed outlier: 3.946A pdb=" N ASN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY A 530 " --> pdb=" O THR A 571 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 655 through 656 removed outlier: 4.723A pdb=" N PHE A 663 " --> pdb=" O GLY A 656 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.577A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.207A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.044A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.979A pdb=" N ALA B 173 " --> pdb=" O TRP B 183 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.649A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B 225 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254 removed outlier: 7.361A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.867A pdb=" N ARG B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.554A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 378 through 381 removed outlier: 3.740A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 33 removed outlier: 4.470A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AC2, first strand: chain 'F' and resid 36 through 37 removed outlier: 3.546A pdb=" N ALA F 30 " --> pdb=" O VAL F 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 230 through 234 removed outlier: 5.674A pdb=" N GLN F 230 " --> pdb=" O HIS F 178 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N HIS F 178 " --> pdb=" O GLN F 230 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY F 232 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU F 176 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN F 175 " --> pdb=" O ASN F 271 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE F 181 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE F 265 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N HIS F 266 " --> pdb=" O PRO F 258 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU F 268 " --> pdb=" O VAL F 256 " (cutoff:3.500A) 626 hydrogen bonds defined for protein. 1752 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: 5.24 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.92: 14124 1.92 - 2.62: 0 2.62 - 3.31: 0 3.31 - 4.01: 0 4.01 - 4.71: 1 Bond restraints: 14125 Sorted by residual: bond pdb=" C SER F 427 " pdb=" O SER F 427 " ideal model delta sigma weight residual 1.231 4.711 -3.480 2.00e-02 2.50e+03 3.03e+04 bond pdb=" N VAL F 192 " pdb=" CA VAL F 192 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.24e-02 6.50e+03 6.77e+00 bond pdb=" N ASN F 193 " pdb=" CA ASN F 193 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.17e+00 bond pdb=" N GLU F 194 " pdb=" CA GLU F 194 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.48e+00 bond pdb=" N SER F 189 " pdb=" CA SER F 189 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.40e+00 ... (remaining 14120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.80: 19168 5.80 - 11.60: 5 11.60 - 17.40: 0 17.40 - 23.21: 0 23.21 - 29.01: 1 Bond angle restraints: 19174 Sorted by residual: angle pdb=" CA SER F 427 " pdb=" C SER F 427 " pdb=" O SER F 427 " ideal model delta sigma weight residual 120.80 91.79 29.01 1.70e+00 3.46e-01 2.91e+02 angle pdb=" N GLN F 191 " pdb=" CA GLN F 191 " pdb=" C GLN F 191 " ideal model delta sigma weight residual 111.07 107.09 3.98 1.07e+00 8.73e-01 1.39e+01 angle pdb=" C GLN A 445 " pdb=" N GLN A 446 " pdb=" CA GLN A 446 " ideal model delta sigma weight residual 122.58 115.54 7.04 2.07e+00 2.33e-01 1.16e+01 angle pdb=" N ILE F 242 " pdb=" CA ILE F 242 " pdb=" C ILE F 242 " ideal model delta sigma weight residual 112.98 109.16 3.82 1.25e+00 6.40e-01 9.35e+00 angle pdb=" CA ARG F 207 " pdb=" CB ARG F 207 " pdb=" CG ARG F 207 " ideal model delta sigma weight residual 114.10 120.14 -6.04 2.00e+00 2.50e-01 9.13e+00 ... (remaining 19169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7594 17.83 - 35.66: 681 35.66 - 53.50: 103 53.50 - 71.33: 21 71.33 - 89.16: 17 Dihedral angle restraints: 8416 sinusoidal: 3309 harmonic: 5107 Sorted by residual: dihedral pdb=" CA ASN B 264 " pdb=" C ASN B 264 " pdb=" N GLY B 265 " pdb=" CA GLY B 265 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLY B 265 " pdb=" C GLY B 265 " pdb=" N ASN B 266 " pdb=" CA ASN B 266 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA PHE A 570 " pdb=" C PHE A 570 " pdb=" N THR A 571 " pdb=" CA THR A 571 " ideal model delta harmonic sigma weight residual -180.00 -163.86 -16.14 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 8413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1324 0.032 - 0.065: 526 0.065 - 0.097: 142 0.097 - 0.129: 104 0.129 - 0.161: 11 Chirality restraints: 2107 Sorted by residual: chirality pdb=" CA VAL F 192 " pdb=" N VAL F 192 " pdb=" C VAL F 192 " pdb=" CB VAL F 192 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CB THR A 62 " pdb=" CA THR A 62 " pdb=" OG1 THR A 62 " pdb=" CG2 THR A 62 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA VAL A 119 " pdb=" N VAL A 119 " pdb=" C VAL A 119 " pdb=" CB VAL A 119 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 2104 not shown) Planarity restraints: 2532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 408 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 409 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 409 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 409 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 778 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 779 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 779 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 779 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 405 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 406 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 406 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 406 " -0.019 5.00e-02 4.00e+02 ... (remaining 2529 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 865 2.73 - 3.28: 13739 3.28 - 3.82: 21736 3.82 - 4.36: 24795 4.36 - 4.90: 43862 Nonbonded interactions: 104997 Sorted by model distance: nonbonded pdb=" O ASP A 28 " pdb=" OG1 THR A 83 " model vdw 2.194 3.040 nonbonded pdb=" OG SER F 220 " pdb=" OD1 ASP F 222 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 674 " pdb=" OD2 ASP A 704 " model vdw 2.232 3.040 nonbonded pdb=" O LYS C 32 " pdb=" OH TYR D 77 " model vdw 2.258 3.040 nonbonded pdb=" OD2 ASP A 582 " pdb=" OG1 THR A 588 " model vdw 2.275 3.040 ... (remaining 104992 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 33.840 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:4.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.029 3.480 14125 Z= 2.768 Angle : 0.589 29.008 19174 Z= 0.329 Chirality : 0.043 0.161 2107 Planarity : 0.004 0.039 2532 Dihedral : 14.130 89.162 5158 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.80 % Favored : 94.14 % Rotamer: Outliers : 0.20 % Allowed : 0.74 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1758 helix: 1.41 (0.24), residues: 457 sheet: 0.03 (0.24), residues: 446 loop : -1.65 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 348 HIS 0.002 0.000 HIS A 677 PHE 0.020 0.001 PHE D 64 TYR 0.023 0.001 TYR A 548 ARG 0.004 0.000 ARG F 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 203 time to evaluate : 1.575 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 273 " (corrupted residue). Skipping it. REVERT: A 480 VAL cc_start: 0.9224 (t) cc_final: 0.8456 (t) REVERT: A 614 ASP cc_start: 0.8290 (m-30) cc_final: 0.7992 (t0) REVERT: B 350 ASN cc_start: 0.8873 (t0) cc_final: 0.8624 (t0) REVERT: E 54 GLN cc_start: 0.6930 (pt0) cc_final: 0.5355 (mt0) REVERT: F 129 ARG cc_start: 0.4649 (ttt-90) cc_final: 0.4344 (ptm160) REVERT: F 138 ILE cc_start: 0.7253 (tp) cc_final: 0.6862 (tt) outliers start: 3 outliers final: 1 residues processed: 204 average time/residue: 0.2421 time to fit residues: 74.5730 Evaluate side-chains 170 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 30.0000 chunk 83 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 538 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.098636 restraints weight = 26271.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.098644 restraints weight = 39904.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.099351 restraints weight = 36637.178| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14125 Z= 0.257 Angle : 0.546 5.514 19174 Z= 0.295 Chirality : 0.043 0.162 2107 Planarity : 0.004 0.041 2532 Dihedral : 4.355 18.786 1939 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.07 % Allowed : 5.17 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.20), residues: 1758 helix: 1.47 (0.23), residues: 462 sheet: 0.05 (0.24), residues: 446 loop : -1.77 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 348 HIS 0.003 0.001 HIS A 677 PHE 0.018 0.001 PHE A 140 TYR 0.013 0.001 TYR A 548 ARG 0.003 0.000 ARG F 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 273 " (corrupted residue). Skipping it. REVERT: A 614 ASP cc_start: 0.8499 (m-30) cc_final: 0.7936 (t0) REVERT: B 278 MET cc_start: 0.7432 (mpp) cc_final: 0.7220 (mpp) REVERT: B 288 ASP cc_start: 0.7948 (t0) cc_final: 0.7740 (m-30) REVERT: B 350 ASN cc_start: 0.8819 (t0) cc_final: 0.8568 (t0) REVERT: D 74 ASP cc_start: 0.8161 (t70) cc_final: 0.7944 (t70) REVERT: D 157 SER cc_start: 0.9387 (p) cc_final: 0.9148 (p) REVERT: E 50 MET cc_start: 0.7105 (mtp) cc_final: 0.6886 (mtp) REVERT: F 78 GLN cc_start: 0.7641 (tp-100) cc_final: 0.7368 (tp-100) REVERT: F 129 ARG cc_start: 0.4660 (ttt-90) cc_final: 0.4212 (ptm160) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.2444 time to fit residues: 73.8760 Evaluate side-chains 168 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 63 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 115 optimal weight: 10.0000 chunk 72 optimal weight: 0.0060 chunk 64 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN E 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101421 restraints weight = 26203.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.101226 restraints weight = 40958.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.102315 restraints weight = 36289.090| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14125 Z= 0.151 Angle : 0.497 5.349 19174 Z= 0.266 Chirality : 0.042 0.158 2107 Planarity : 0.004 0.047 2532 Dihedral : 4.148 16.697 1939 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.20), residues: 1758 helix: 1.72 (0.24), residues: 456 sheet: 0.10 (0.24), residues: 453 loop : -1.71 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 317 HIS 0.003 0.000 HIS F 178 PHE 0.012 0.001 PHE A 738 TYR 0.012 0.001 TYR A 509 ARG 0.003 0.000 ARG F 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 273 " (corrupted residue). Skipping it. REVERT: A 480 VAL cc_start: 0.9208 (t) cc_final: 0.8597 (t) REVERT: A 548 TYR cc_start: 0.7891 (t80) cc_final: 0.7643 (t80) REVERT: A 614 ASP cc_start: 0.8338 (m-30) cc_final: 0.7940 (t0) REVERT: A 738 PHE cc_start: 0.9097 (p90) cc_final: 0.8844 (p90) REVERT: B 288 ASP cc_start: 0.8004 (t0) cc_final: 0.7705 (m-30) REVERT: B 350 ASN cc_start: 0.8762 (t0) cc_final: 0.8539 (t0) REVERT: D 157 SER cc_start: 0.9365 (p) cc_final: 0.9104 (p) REVERT: E 50 MET cc_start: 0.7176 (mtp) cc_final: 0.6737 (mtp) REVERT: E 93 LEU cc_start: 0.8645 (mm) cc_final: 0.8386 (mt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2483 time to fit residues: 83.2737 Evaluate side-chains 185 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 10.0000 chunk 14 optimal weight: 0.0020 chunk 50 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 0.2980 chunk 112 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 overall best weight: 2.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN A 563 ASN A 606 ASN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.099326 restraints weight = 26413.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.098646 restraints weight = 35406.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.099390 restraints weight = 37486.586| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14125 Z= 0.262 Angle : 0.551 5.331 19174 Z= 0.294 Chirality : 0.044 0.160 2107 Planarity : 0.004 0.047 2532 Dihedral : 4.405 20.235 1939 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1758 helix: 1.57 (0.24), residues: 457 sheet: -0.04 (0.24), residues: 448 loop : -1.71 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 348 HIS 0.003 0.001 HIS A 677 PHE 0.014 0.001 PHE A 394 TYR 0.022 0.001 TYR D 36 ARG 0.006 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 273 " (corrupted residue). Skipping it. REVERT: A 90 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6390 (mt-10) REVERT: A 548 TYR cc_start: 0.7903 (t80) cc_final: 0.7693 (t80) REVERT: A 614 ASP cc_start: 0.8334 (m-30) cc_final: 0.7851 (t0) REVERT: B 288 ASP cc_start: 0.7993 (t0) cc_final: 0.7685 (m-30) REVERT: D 157 SER cc_start: 0.9412 (p) cc_final: 0.9150 (p) REVERT: E 50 MET cc_start: 0.7214 (mtp) cc_final: 0.6719 (mtp) outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.2436 time to fit residues: 75.9596 Evaluate side-chains 167 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 31 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN A 563 ASN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099971 restraints weight = 26561.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.098921 restraints weight = 34403.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099583 restraints weight = 35273.694| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14125 Z= 0.219 Angle : 0.530 5.467 19174 Z= 0.285 Chirality : 0.043 0.150 2107 Planarity : 0.004 0.042 2532 Dihedral : 4.365 18.999 1939 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1758 helix: 1.63 (0.24), residues: 457 sheet: -0.04 (0.24), residues: 447 loop : -1.68 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 348 HIS 0.003 0.001 HIS F 178 PHE 0.013 0.001 PHE A 394 TYR 0.021 0.001 TYR D 36 ARG 0.005 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 273 " (corrupted residue). Skipping it. REVERT: A 480 VAL cc_start: 0.9217 (t) cc_final: 0.8765 (t) REVERT: A 614 ASP cc_start: 0.8361 (m-30) cc_final: 0.7855 (t0) REVERT: B 288 ASP cc_start: 0.7966 (t0) cc_final: 0.7700 (m-30) REVERT: B 306 MET cc_start: 0.8118 (mtt) cc_final: 0.7912 (mtt) REVERT: B 350 ASN cc_start: 0.8825 (t0) cc_final: 0.8540 (t0) REVERT: D 38 THR cc_start: 0.8096 (p) cc_final: 0.7833 (t) REVERT: D 157 SER cc_start: 0.9411 (p) cc_final: 0.9129 (p) REVERT: E 50 MET cc_start: 0.7202 (mtp) cc_final: 0.6675 (mtp) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.2399 time to fit residues: 73.7548 Evaluate side-chains 169 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 58.0863 > 50: distance: 58 - 104: 11.970 distance: 61 - 101: 10.118 distance: 71 - 87: 10.243 distance: 74 - 84: 10.407 distance: 82 - 84: 9.227 distance: 84 - 85: 10.512 distance: 85 - 86: 4.197 distance: 85 - 88: 6.433 distance: 86 - 87: 9.002 distance: 86 - 94: 5.129 distance: 88 - 89: 5.978 distance: 89 - 90: 3.683 distance: 89 - 91: 3.248 distance: 90 - 92: 3.881 distance: 94 - 95: 4.615 distance: 94 - 190: 15.050 distance: 95 - 98: 10.093 distance: 96 - 97: 5.804 distance: 96 - 101: 7.724 distance: 97 - 187: 11.707 distance: 98 - 99: 14.656 distance: 98 - 100: 10.806 distance: 101 - 102: 7.635 distance: 102 - 103: 12.436 distance: 102 - 105: 12.061 distance: 103 - 104: 8.445 distance: 103 - 113: 22.074 distance: 105 - 106: 4.616 distance: 106 - 107: 10.547 distance: 106 - 108: 5.191 distance: 107 - 109: 5.732 distance: 108 - 110: 5.343 distance: 109 - 111: 12.210 distance: 110 - 111: 5.928 distance: 111 - 112: 9.419 distance: 113 - 114: 11.108 distance: 113 - 173: 18.024 distance: 114 - 115: 12.269 distance: 114 - 117: 16.987 distance: 115 - 116: 12.547 distance: 115 - 121: 12.785 distance: 116 - 170: 25.351 distance: 117 - 118: 6.540 distance: 117 - 119: 18.010 distance: 118 - 120: 30.846 distance: 121 - 122: 9.949 distance: 122 - 123: 35.094 distance: 123 - 124: 28.286 distance: 123 - 125: 38.005 distance: 125 - 126: 9.011 distance: 126 - 127: 23.435 distance: 126 - 129: 41.339 distance: 127 - 128: 9.718 distance: 127 - 131: 7.914 distance: 129 - 130: 23.394 distance: 131 - 132: 19.175 distance: 132 - 133: 12.752 distance: 132 - 135: 7.542 distance: 133 - 134: 19.435 distance: 133 - 140: 16.966 distance: 135 - 136: 12.887 distance: 136 - 137: 28.438 distance: 137 - 139: 4.892 distance: 140 - 141: 18.901 distance: 141 - 142: 26.105 distance: 141 - 144: 8.768 distance: 142 - 143: 12.414 distance: 142 - 149: 8.755 distance: 144 - 145: 19.610 distance: 145 - 146: 15.979 distance: 146 - 147: 11.112 distance: 147 - 148: 8.724 distance: 149 - 150: 14.503 distance: 150 - 151: 34.603 distance: 150 - 153: 30.304 distance: 151 - 152: 19.319 distance: 151 - 154: 13.856 distance: 154 - 155: 5.228 distance: 155 - 156: 12.742 distance: 155 - 158: 6.781 distance: 156 - 157: 9.410 distance: 156 - 163: 7.959 distance: 158 - 159: 28.939 distance: 159 - 160: 36.417 distance: 160 - 161: 41.727 distance: 160 - 162: 13.916