Starting phenix.real_space_refine on Fri Dec 8 01:37:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx4_32168/12_2023/7vx4_32168.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx4_32168/12_2023/7vx4_32168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx4_32168/12_2023/7vx4_32168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx4_32168/12_2023/7vx4_32168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx4_32168/12_2023/7vx4_32168.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx4_32168/12_2023/7vx4_32168.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4152 2.51 5 N 1070 2.21 5 O 1233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6493 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "E" Number of atoms: 1545 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 194, 1539 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Conformer: "B" Number of residues, atoms: 194, 1539 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} bond proxies already assigned to first conformer: 1576 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} 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 Chain: "E" 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 Time building chain proxies: 6.72, per 1000 atoms: 1.03 Number of scatterers: 6493 At special positions: 0 Unit cell: (77.603, 101.649, 118.044, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1233 8.00 N 1070 7.00 C 4152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 902 " - " ASN A 546 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 53 " " NAG E1301 " - " ASN E 343 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 58.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.660A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.954A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.742A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.511A pdb=" N LYS A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.826A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.560A pdb=" N LYS A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.615A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.750A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.677A pdb=" N TRP A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.598A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.599A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.780A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.824A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.098A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 removed outlier: 3.579A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 414 removed outlier: 4.396A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.599A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.407A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.750A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.990A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.773A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.729A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.648A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.948A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.585A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 385 through 389 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.102A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.140A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.923A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.759A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 273 hydrogen bonds defined for protein. 769 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: 1.62 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2081 1.34 - 1.46: 1727 1.46 - 1.58: 2810 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6676 Sorted by residual: bond pdb=" C1 NAG A 905 " pdb=" O5 NAG A 905 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG A 904 " pdb=" O5 NAG A 904 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C1 NAG A 903 " pdb=" O5 NAG A 903 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C5 NAG A 905 " pdb=" O5 NAG A 905 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.38e+00 ... (remaining 6671 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.54: 212 106.54 - 113.40: 3494 113.40 - 120.26: 2532 120.26 - 127.12: 2742 127.12 - 133.98: 98 Bond angle restraints: 9078 Sorted by residual: angle pdb=" C PHE E 497 " pdb=" N GLN E 498 " pdb=" CA GLN E 498 " ideal model delta sigma weight residual 121.98 131.85 -9.87 3.11e+00 1.03e-01 1.01e+01 angle pdb=" N TYR E 505 " pdb=" CA TYR E 505 " pdb=" C TYR E 505 " ideal model delta sigma weight residual 111.36 114.77 -3.41 1.09e+00 8.42e-01 9.78e+00 angle pdb=" N ASP A 136 " pdb=" CA ASP A 136 " pdb=" C ASP A 136 " ideal model delta sigma weight residual 111.07 114.15 -3.08 1.07e+00 8.73e-01 8.31e+00 angle pdb=" N VAL A 293 " pdb=" CA VAL A 293 " pdb=" C VAL A 293 " ideal model delta sigma weight residual 112.83 110.26 2.57 9.90e-01 1.02e+00 6.75e+00 angle pdb=" C LYS A 363 " pdb=" N VAL A 364 " pdb=" CA VAL A 364 " ideal model delta sigma weight residual 122.43 119.17 3.26 1.26e+00 6.30e-01 6.71e+00 ... (remaining 9073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 3883 16.02 - 32.05: 77 32.05 - 48.07: 33 48.07 - 64.09: 8 64.09 - 80.12: 3 Dihedral angle restraints: 4004 sinusoidal: 1675 harmonic: 2329 Sorted by residual: dihedral pdb=" CA PHE E 497 " pdb=" C PHE E 497 " pdb=" N GLN E 498 " pdb=" CA GLN E 498 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA PRO A 146 " pdb=" C PRO A 146 " pdb=" N GLY A 147 " pdb=" CA GLY A 147 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ALA E 352 " pdb=" C ALA E 352 " pdb=" N TRP E 353 " pdb=" CA TRP E 353 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 584 0.030 - 0.061: 242 0.061 - 0.091: 91 0.091 - 0.121: 42 0.121 - 0.151: 4 Chirality restraints: 963 Sorted by residual: chirality pdb=" C1 NAG E1301 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG E1301 " pdb=" O5 NAG E1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA TYR E 505 " pdb=" N TYR E 505 " pdb=" C TYR E 505 " pdb=" CB TYR E 505 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 960 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 504 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C GLY E 504 " -0.029 2.00e-02 2.50e+03 pdb=" O GLY E 504 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR E 505 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 611 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO A 612 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 612 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 612 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 495 " -0.012 2.00e-02 2.50e+03 1.05e-02 2.19e+00 pdb=" CG TYR E 495 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR E 495 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR E 495 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 495 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 495 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 495 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 495 " 0.001 2.00e-02 2.50e+03 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 87 2.65 - 3.21: 6043 3.21 - 3.77: 9658 3.77 - 4.34: 13646 4.34 - 4.90: 22092 Nonbonded interactions: 51526 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.082 2.230 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.189 2.230 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.199 2.440 nonbonded pdb=" OD2 ASP E 398 " pdb=" OH TYR E 423 " model vdw 2.225 2.440 nonbonded pdb=" O LEU A 156 " pdb=" OH TYR A 252 " model vdw 2.234 2.440 ... (remaining 51521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.50 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: 7.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 10.620 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 25.960 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6676 Z= 0.182 Angle : 0.627 9.874 9078 Z= 0.393 Chirality : 0.042 0.151 963 Planarity : 0.004 0.038 1172 Dihedral : 8.878 80.115 2491 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 0.89 % Favored : 98.98 % Rotamer: Outliers : 0.14 % Allowed : 0.29 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -2.27 (0.26), residues: 789 helix: -2.59 (0.20), residues: 372 sheet: -0.28 (0.66), residues: 50 loop : -0.21 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 302 HIS 0.003 0.001 HIS A 34 PHE 0.020 0.002 PHE E 497 TYR 0.025 0.001 TYR E 495 ARG 0.006 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.2068 time to fit residues: 61.9736 Evaluate side-chains 117 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 0.0170 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 0.1980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 61 ASN A 524 GLN A 598 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6676 Z= 0.186 Angle : 0.632 8.271 9078 Z= 0.329 Chirality : 0.044 0.169 963 Planarity : 0.005 0.033 1172 Dihedral : 5.684 43.733 969 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 3.45 % Allowed : 12.07 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.46 (0.28), residues: 789 helix: -0.57 (0.24), residues: 380 sheet: -0.21 (0.64), residues: 44 loop : 0.22 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 594 HIS 0.003 0.001 HIS A 535 PHE 0.028 0.002 PHE A 308 TYR 0.024 0.002 TYR E 495 ARG 0.007 0.001 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 142 average time/residue: 0.1649 time to fit residues: 32.5499 Evaluate side-chains 110 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0633 time to fit residues: 2.5399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.0670 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 0.2980 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 101 GLN A 598 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6676 Z= 0.214 Angle : 0.603 9.305 9078 Z= 0.312 Chirality : 0.044 0.201 963 Planarity : 0.004 0.034 1172 Dihedral : 5.128 37.546 969 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.01 % Allowed : 12.21 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.03 (0.29), residues: 789 helix: -0.01 (0.26), residues: 390 sheet: -0.08 (0.65), residues: 45 loop : 0.21 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 594 HIS 0.003 0.001 HIS A 535 PHE 0.023 0.002 PHE E 497 TYR 0.020 0.002 TYR E 495 ARG 0.006 0.001 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 0.780 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 116 average time/residue: 0.1669 time to fit residues: 26.8494 Evaluate side-chains 98 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.728 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0724 time to fit residues: 1.7247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.0670 chunk 20 optimal weight: 0.0470 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6676 Z= 0.188 Angle : 0.592 9.705 9078 Z= 0.299 Chirality : 0.044 0.177 963 Planarity : 0.004 0.035 1172 Dihedral : 4.877 37.311 969 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.87 % Allowed : 14.08 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.29), residues: 789 helix: 0.20 (0.26), residues: 400 sheet: 0.15 (0.70), residues: 49 loop : 0.17 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 594 HIS 0.003 0.001 HIS A 535 PHE 0.019 0.002 PHE E 497 TYR 0.019 0.001 TYR E 495 ARG 0.005 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 104 average time/residue: 0.1634 time to fit residues: 24.3799 Evaluate side-chains 97 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.689 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0697 time to fit residues: 1.7783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 508 ASN A 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6676 Z= 0.218 Angle : 0.583 8.286 9078 Z= 0.299 Chirality : 0.044 0.201 963 Planarity : 0.004 0.035 1172 Dihedral : 4.718 31.871 969 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.30 % Allowed : 13.79 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.18 (0.29), residues: 789 helix: 0.28 (0.26), residues: 403 sheet: 0.08 (0.71), residues: 49 loop : 0.14 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 478 HIS 0.003 0.001 HIS A 535 PHE 0.020 0.002 PHE E 497 TYR 0.018 0.002 TYR E 495 ARG 0.004 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.782 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 104 average time/residue: 0.1741 time to fit residues: 25.2596 Evaluate side-chains 90 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.723 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0653 time to fit residues: 1.4775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6676 Z= 0.260 Angle : 0.610 8.546 9078 Z= 0.312 Chirality : 0.045 0.191 963 Planarity : 0.004 0.036 1172 Dihedral : 4.779 30.459 969 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.29 % Allowed : 15.37 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.05 (0.29), residues: 789 helix: 0.14 (0.26), residues: 404 sheet: -0.22 (0.70), residues: 49 loop : -0.01 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 302 HIS 0.003 0.001 HIS A 505 PHE 0.020 0.002 PHE E 497 TYR 0.020 0.002 TYR E 495 ARG 0.004 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.799 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 102 average time/residue: 0.2009 time to fit residues: 28.0060 Evaluate side-chains 90 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0797 time to fit residues: 1.7514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.7980 chunk 42 optimal weight: 0.0770 chunk 63 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6676 Z= 0.206 Angle : 0.607 7.377 9078 Z= 0.309 Chirality : 0.045 0.309 963 Planarity : 0.004 0.036 1172 Dihedral : 5.838 54.155 969 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.86 % Allowed : 15.95 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.03 (0.29), residues: 789 helix: 0.23 (0.26), residues: 406 sheet: -0.32 (0.71), residues: 49 loop : 0.02 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 302 HIS 0.003 0.001 HIS A 505 PHE 0.017 0.002 PHE A 308 TYR 0.015 0.001 TYR E 508 ARG 0.005 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.650 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 95 average time/residue: 0.1758 time to fit residues: 22.9764 Evaluate side-chains 87 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0635 time to fit residues: 1.1306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.9763 > 50: distance: 77 - 97: 17.710 distance: 93 - 97: 19.635 distance: 97 - 98: 25.355 distance: 98 - 99: 37.529 distance: 98 - 101: 15.400 distance: 99 - 100: 12.136 distance: 99 - 105: 25.011 distance: 101 - 102: 23.115 distance: 102 - 103: 22.486 distance: 102 - 104: 14.824 distance: 105 - 106: 19.202 distance: 106 - 107: 26.656 distance: 106 - 109: 18.173 distance: 107 - 108: 26.607 distance: 107 - 117: 40.796 distance: 109 - 110: 8.665 distance: 110 - 111: 6.562 distance: 110 - 112: 4.639 distance: 111 - 113: 24.697 distance: 112 - 114: 16.341 distance: 113 - 115: 5.696 distance: 114 - 115: 9.283 distance: 115 - 116: 10.135 distance: 117 - 118: 13.160 distance: 118 - 119: 9.019 distance: 118 - 121: 6.900 distance: 119 - 120: 11.294 distance: 119 - 126: 54.249 distance: 121 - 122: 17.523 distance: 122 - 123: 12.246 distance: 123 - 124: 12.634 distance: 124 - 125: 50.682 distance: 126 - 127: 40.110 distance: 127 - 128: 17.879 distance: 127 - 130: 15.430 distance: 128 - 129: 3.720 distance: 128 - 134: 24.197 distance: 130 - 131: 17.951 distance: 131 - 132: 38.031 distance: 131 - 133: 61.735 distance: 134 - 135: 12.304 distance: 134 - 140: 10.432 distance: 135 - 136: 17.055 distance: 135 - 138: 12.540 distance: 136 - 137: 16.217 distance: 136 - 141: 25.390 distance: 138 - 139: 4.315 distance: 139 - 140: 17.706 distance: 141 - 142: 27.452 distance: 142 - 143: 15.353 distance: 142 - 145: 17.806 distance: 143 - 144: 13.458 distance: 143 - 149: 25.177 distance: 145 - 146: 15.613 distance: 146 - 147: 25.871 distance: 146 - 148: 21.070 distance: 149 - 150: 12.935 distance: 150 - 151: 12.407 distance: 150 - 153: 4.142 distance: 151 - 152: 35.352 distance: 151 - 157: 18.228 distance: 153 - 154: 13.049 distance: 154 - 155: 4.661 distance: 154 - 156: 19.702 distance: 157 - 158: 18.846 distance: 158 - 159: 13.475 distance: 158 - 161: 7.910 distance: 159 - 160: 21.590 distance: 159 - 168: 23.150 distance: 161 - 162: 16.669 distance: 162 - 163: 24.586 distance: 162 - 164: 6.208 distance: 163 - 165: 15.688 distance: 164 - 166: 19.670 distance: 165 - 167: 15.669 distance: 166 - 167: 19.007 distance: 168 - 169: 6.444 distance: 169 - 172: 14.855 distance: 170 - 171: 31.006 distance: 170 - 175: 19.782 distance: 172 - 173: 8.553 distance: 172 - 174: 12.397 distance: 175 - 176: 17.827 distance: 176 - 177: 9.536 distance: 177 - 178: 14.121 distance: 177 - 179: 12.525