Starting phenix.real_space_refine on Fri Dec 8 20:16:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx4_30895/12_2023/7dx4_30895_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx4_30895/12_2023/7dx4_30895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx4_30895/12_2023/7dx4_30895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx4_30895/12_2023/7dx4_30895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx4_30895/12_2023/7dx4_30895_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx4_30895/12_2023/7dx4_30895_neut.pdb" } resolution = 3.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 805 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 5241 2.51 5 N 1364 2.21 5 O 1586 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 "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 56": "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: 8234 Number of models: 1 Model: "" Number of chains: 6 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: 1542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Conformer: "B" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} bond proxies already assigned to first conformer: 1572 Chain: "H" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 939 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 806 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 7.33, per 1000 atoms: 0.89 Number of scatterers: 8234 At special positions: 0 Unit cell: (144.56, 91.52, 78, 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 43 16.00 O 1586 8.00 N 1364 7.00 C 5241 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 97 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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 701 " - " ASN A 546 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 322 " " NAG A 704 " - " ASN A 53 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 2.7 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1902 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 12 sheets defined 43.9% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.988A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.534A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.631A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 4.132A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.936A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.510A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.613A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 193 removed outlier: 3.572A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.627A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.715A pdb=" N HIS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.817A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (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 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.558A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.917A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.709A pdb=" N ALA A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.865A 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 400 through 411 removed outlier: 3.859A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.966A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.392A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 465 " --> pdb=" O TRP A 461 " (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: 3.664A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 515 Processing helix chain 'A' and resid 516 through 531 removed outlier: 3.760A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.800A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.682A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.645A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.606A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 370' Processing helix chain 'E' and resid 385 through 390 removed outlier: 3.554A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 408 removed outlier: 3.788A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.653A pdb=" N GLN E 506 " --> pdb=" O VAL E 503 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.760A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.635A 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 350 Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.817A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS E 432 " --> pdb=" O LEU E 513 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.917A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'H' and resid 6 through 7 removed outlier: 4.157A pdb=" N VAL H 21 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.568A pdb=" N VAL H 38 " --> pdb=" O TYR H 96 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE H 35 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLY H 51 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.794A pdb=" N GLY L 99 " --> pdb=" O ASP L 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 17 through 21 removed outlier: 3.612A pdb=" N SER L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2374 1.33 - 1.45: 1789 1.45 - 1.58: 4226 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 8455 Sorted by residual: bond pdb=" C GLY A 319 " pdb=" N LEU A 320 " ideal model delta sigma weight residual 1.330 1.362 -0.032 1.37e-02 5.33e+03 5.36e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.36e+00 bond pdb=" CB MET A 579 " pdb=" CG MET A 579 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.13e+00 bond pdb=" C1 NAG A 704 " pdb=" O5 NAG A 704 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 ... (remaining 8450 not shown) Histogram of bond angle deviations from ideal: 97.18 - 104.56: 146 104.56 - 111.94: 3843 111.94 - 119.32: 2945 119.32 - 126.70: 4411 126.70 - 134.08: 146 Bond angle restraints: 11491 Sorted by residual: angle pdb=" N ASP H 113 " pdb=" CA ASP H 113 " pdb=" C ASP H 113 " ideal model delta sigma weight residual 114.16 102.73 11.43 1.48e+00 4.57e-01 5.97e+01 angle pdb=" C PHE H 112 " pdb=" N ASP H 113 " pdb=" CA ASP H 113 " ideal model delta sigma weight residual 120.70 131.47 -10.77 1.63e+00 3.76e-01 4.36e+01 angle pdb=" N ASN E 440 " pdb=" CA ASN E 440 " pdb=" CB ASN E 440 " ideal model delta sigma weight residual 110.13 102.65 7.48 1.48e+00 4.57e-01 2.56e+01 angle pdb=" C GLY L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C ILE L 50 " pdb=" N TYR L 51 " pdb=" CA TYR L 51 " ideal model delta sigma weight residual 120.94 128.52 -7.58 1.57e+00 4.06e-01 2.33e+01 ... (remaining 11486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.43: 4892 20.43 - 40.85: 119 40.85 - 61.28: 23 61.28 - 81.71: 4 81.71 - 102.13: 8 Dihedral angle restraints: 5046 sinusoidal: 2058 harmonic: 2988 Sorted by residual: dihedral pdb=" CA PHE H 112 " pdb=" C PHE H 112 " pdb=" N ASP H 113 " pdb=" CA ASP H 113 " ideal model delta harmonic sigma weight residual 180.00 127.40 52.60 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA LEU L 48 " pdb=" C LEU L 48 " pdb=" N LEU L 49 " pdb=" CA LEU L 49 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ALA H 108 " pdb=" C ALA H 108 " pdb=" N ALA H 109 " pdb=" CA ALA H 109 " ideal model delta harmonic sigma weight residual -180.00 -152.19 -27.81 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 5043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1030 0.073 - 0.145: 173 0.145 - 0.218: 16 0.218 - 0.291: 4 0.291 - 0.363: 2 Chirality restraints: 1225 Sorted by residual: chirality pdb=" CG LEU A 558 " pdb=" CB LEU A 558 " pdb=" CD1 LEU A 558 " pdb=" CD2 LEU A 558 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB ILE H 35 " pdb=" CA ILE H 35 " pdb=" CG1 ILE H 35 " pdb=" CG2 ILE H 35 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CG LEU A 333 " pdb=" CB LEU A 333 " pdb=" CD1 LEU A 333 " pdb=" CD2 LEU A 333 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1222 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 440 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" CG ASN E 440 " -0.064 2.00e-02 2.50e+03 pdb=" OD1 ASN E 440 " 0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN E 440 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 497 " 0.019 2.00e-02 2.50e+03 2.14e-02 8.02e+00 pdb=" CG PHE E 497 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE E 497 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE E 497 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE E 497 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE E 497 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE E 497 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.046 5.00e-02 4.00e+02 6.88e-02 7.57e+00 pdb=" N PRO A 583 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.039 5.00e-02 4.00e+02 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 0.77 - 1.59: 5 1.59 - 2.42: 43 2.42 - 3.25: 8163 3.25 - 4.07: 21544 4.07 - 4.90: 39724 Warning: very small nonbonded interaction distances. Nonbonded interactions: 69479 Sorted by model distance: nonbonded pdb=" C LEU H 4 " pdb=" OG SER H 26 " model vdw 0.766 3.270 nonbonded pdb=" N LEU H 5 " pdb=" OG SER H 26 " model vdw 0.943 2.520 nonbonded pdb=" CA LEU H 5 " pdb=" CB SER H 26 " model vdw 1.145 3.870 nonbonded pdb=" O LEU H 4 " pdb=" OG SER H 26 " model vdw 1.387 2.440 nonbonded pdb=" O THR H 29 " pdb=" NH2 ARG H 99 " model vdw 1.521 2.520 ... (remaining 69474 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 6.150 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 28.730 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.007 0.062 8455 Z= 0.430 Angle : 1.002 11.433 11491 Z= 0.575 Chirality : 0.057 0.363 1225 Planarity : 0.007 0.069 1484 Dihedral : 11.251 102.133 3117 Min Nonbonded Distance : 0.766 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.99 % Favored : 93.72 % Rotamer: Outliers : 0.23 % Allowed : 1.25 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -4.20 (0.21), residues: 1021 helix: -3.94 (0.14), residues: 368 sheet: -2.19 (0.43), residues: 137 loop : -1.95 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 302 HIS 0.014 0.002 HIS A 401 PHE 0.049 0.004 PHE E 497 TYR 0.037 0.004 TYR E 495 ARG 0.019 0.002 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2170 time to fit residues: 65.0753 Evaluate side-chains 127 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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: 65.0451 > 50: distance: 8 - 13: 25.888 distance: 9 - 151: 3.393 distance: 13 - 14: 14.804 distance: 14 - 15: 27.498 distance: 14 - 17: 41.613 distance: 15 - 16: 12.377 distance: 15 - 19: 12.941 distance: 17 - 18: 34.123 distance: 19 - 20: 18.681 distance: 19 - 154: 35.173 distance: 20 - 21: 19.023 distance: 21 - 22: 56.852 distance: 21 - 23: 44.135 distance: 23 - 24: 9.768 distance: 24 - 25: 31.708 distance: 24 - 27: 31.828 distance: 25 - 26: 33.566 distance: 25 - 28: 55.673 distance: 28 - 29: 43.065 distance: 28 - 34: 29.165 distance: 29 - 30: 55.185 distance: 30 - 35: 38.830 distance: 32 - 33: 7.919 distance: 33 - 34: 13.358 distance: 35 - 36: 39.594 distance: 36 - 37: 27.075 distance: 37 - 38: 16.926 distance: 37 - 39: 35.248 distance: 39 - 40: 7.698 distance: 40 - 43: 25.534 distance: 41 - 42: 40.755 distance: 43 - 44: 22.562 distance: 44 - 45: 28.587 distance: 45 - 47: 33.653 distance: 48 - 49: 32.434 distance: 49 - 50: 22.626 distance: 49 - 52: 25.685 distance: 50 - 51: 28.302 distance: 50 - 59: 18.835 distance: 52 - 53: 22.226 distance: 53 - 54: 34.348 distance: 54 - 55: 9.833 distance: 55 - 56: 26.181 distance: 56 - 57: 17.641 distance: 56 - 58: 23.824 distance: 59 - 60: 3.271 distance: 59 - 117: 31.376 distance: 60 - 61: 22.395 distance: 60 - 63: 6.289 distance: 61 - 62: 7.721 distance: 61 - 66: 39.831 distance: 62 - 114: 32.126 distance: 63 - 64: 54.737 distance: 63 - 65: 27.098 distance: 66 - 67: 36.373 distance: 67 - 68: 4.219 distance: 68 - 69: 4.319 distance: 68 - 73: 37.716 distance: 73 - 74: 5.354 distance: 73 - 105: 36.922 distance: 74 - 75: 18.904 distance: 75 - 76: 36.550 distance: 75 - 81: 22.196 distance: 76 - 102: 34.069 distance: 77 - 78: 10.092 distance: 77 - 79: 57.079 distance: 78 - 80: 43.947