Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 09:49:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psl_13613/07_2023/7psl_13613_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psl_13613/07_2023/7psl_13613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psl_13613/07_2023/7psl_13613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psl_13613/07_2023/7psl_13613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psl_13613/07_2023/7psl_13613_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psl_13613/07_2023/7psl_13613_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.070 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 P 4 5.49 5 S 34 5.16 5 C 6190 2.51 5 N 1634 2.21 5 O 1750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 430": "OE1" <-> "OE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 541": "OE1" <-> "OE2" Residue "A GLU 568": "OE1" <-> "OE2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "B GLU 430": "OE1" <-> "OE2" Residue "B GLU 439": "OE1" <-> "OE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B GLU 568": "OE1" <-> "OE2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B GLU 683": "OE1" <-> "OE2" Residue "B GLU 689": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 9612 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4756 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 17, 'TRANS': 582} Chain: "B" Number of atoms: 4756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4756 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 17, 'TRANS': 582} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'LOP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'LOP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.26, per 1000 atoms: 0.55 Number of scatterers: 9612 At special positions: 0 Unit cell: (109.647, 76.167, 142.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 4 15.00 O 1750 8.00 N 1634 7.00 C 6190 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 - 3.50 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 Time building additional restraints: 4.19 Conformation dependent library (CDL) restraints added in 1.4 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 2 sheets defined 63.2% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 93 through 98 Processing helix chain 'A' and resid 105 through 139 Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 152 through 200 removed outlier: 4.073A pdb=" N THR A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 200 " --> pdb=" O GLN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 211 through 233 Processing helix chain 'A' and resid 237 through 253 Processing helix chain 'A' and resid 256 through 303 removed outlier: 3.519A pdb=" N ALA A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 315 through 367 removed outlier: 3.939A pdb=" N ILE A 366 " --> pdb=" O CYS A 362 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY A 367 " --> pdb=" O THR A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 413 Proline residue: A 388 - end of helix removed outlier: 5.535A pdb=" N PHE A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A 400 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 505 through 511 removed outlier: 4.351A pdb=" N VAL A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 533 removed outlier: 4.741A pdb=" N GLY A 533 " --> pdb=" O ASN A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 552 through 555 No H-bonds generated for 'chain 'A' and resid 552 through 555' Processing helix chain 'A' and resid 575 through 589 Processing helix chain 'A' and resid 605 through 618 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 666 through 690 Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 105 through 139 Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 152 through 200 removed outlier: 4.074A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 200 " --> pdb=" O GLN B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 211 through 233 Processing helix chain 'B' and resid 237 through 253 Processing helix chain 'B' and resid 256 through 303 removed outlier: 3.518A pdb=" N ALA B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 315 through 367 removed outlier: 3.938A pdb=" N ILE B 366 " --> pdb=" O CYS B 362 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY B 367 " --> pdb=" O THR B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 413 Proline residue: B 388 - end of helix removed outlier: 5.535A pdb=" N PHE B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG B 397 " --> pdb=" O GLY B 393 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 398 " --> pdb=" O SER B 394 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN B 401 " --> pdb=" O ARG B 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 412 " --> pdb=" O THR B 408 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 505 through 511 removed outlier: 4.351A pdb=" N VAL B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 533 removed outlier: 4.741A pdb=" N GLY B 533 " --> pdb=" O ASN B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 548 Processing helix chain 'B' and resid 552 through 555 No H-bonds generated for 'chain 'B' and resid 552 through 555' Processing helix chain 'B' and resid 575 through 589 Processing helix chain 'B' and resid 605 through 618 Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 656 through 660 Processing helix chain 'B' and resid 666 through 690 Processing sheet with id= A, first strand: chain 'A' and resid 642 through 645 removed outlier: 6.224A pdb=" N ALA A 466 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU A 645 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 468 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 642 through 645 removed outlier: 6.224A pdb=" N ALA B 466 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU B 645 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 468 " --> pdb=" O LEU B 645 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1728 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: 2.91 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1552 1.31 - 1.43: 2487 1.43 - 1.56: 5683 1.56 - 1.68: 4 1.68 - 1.81: 62 Bond restraints: 9788 Sorted by residual: bond pdb=" C24 LOP B 701 " pdb=" O6 LOP B 701 " ideal model delta sigma weight residual 1.325 1.397 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C24 LOP A 701 " pdb=" O6 LOP A 701 " ideal model delta sigma weight residual 1.325 1.397 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C6 LOP A 701 " pdb=" O5 LOP A 701 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C6 LOP B 701 " pdb=" O5 LOP B 701 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O3 PO4 A 702 " pdb=" P PO4 A 702 " ideal model delta sigma weight residual 1.569 1.519 0.050 2.00e-02 2.50e+03 6.23e+00 ... (remaining 9783 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.28: 118 105.28 - 112.45: 5188 112.45 - 119.62: 3063 119.62 - 126.79: 4749 126.79 - 133.96: 108 Bond angle restraints: 13226 Sorted by residual: angle pdb=" N ILE B 526 " pdb=" CA ILE B 526 " pdb=" C ILE B 526 " ideal model delta sigma weight residual 113.42 108.14 5.28 1.17e+00 7.31e-01 2.04e+01 angle pdb=" N ILE A 526 " pdb=" CA ILE A 526 " pdb=" C ILE A 526 " ideal model delta sigma weight residual 113.42 108.14 5.28 1.17e+00 7.31e-01 2.04e+01 angle pdb=" N ILE B 154 " pdb=" CA ILE B 154 " pdb=" C ILE B 154 " ideal model delta sigma weight residual 112.96 109.16 3.80 1.00e+00 1.00e+00 1.44e+01 angle pdb=" N ILE A 154 " pdb=" CA ILE A 154 " pdb=" C ILE A 154 " ideal model delta sigma weight residual 112.96 109.16 3.80 1.00e+00 1.00e+00 1.44e+01 angle pdb=" O3 LOP A 701 " pdb=" P1 LOP A 701 " pdb=" O4 LOP A 701 " ideal model delta sigma weight residual 120.67 109.36 11.31 3.00e+00 1.11e-01 1.42e+01 ... (remaining 13221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 5152 17.54 - 35.07: 570 35.07 - 52.61: 126 52.61 - 70.14: 22 70.14 - 87.68: 4 Dihedral angle restraints: 5874 sinusoidal: 2400 harmonic: 3474 Sorted by residual: dihedral pdb=" CA ASP A 374 " pdb=" CB ASP A 374 " pdb=" CG ASP A 374 " pdb=" OD1 ASP A 374 " ideal model delta sinusoidal sigma weight residual -30.00 -89.21 59.21 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP B 374 " pdb=" CB ASP B 374 " pdb=" CG ASP B 374 " pdb=" OD1 ASP B 374 " ideal model delta sinusoidal sigma weight residual -30.00 -89.18 59.18 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ARG B 484 " pdb=" C ARG B 484 " pdb=" N PHE B 485 " pdb=" CA PHE B 485 " ideal model delta harmonic sigma weight residual 180.00 164.32 15.68 0 5.00e+00 4.00e-02 9.83e+00 ... (remaining 5871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1096 0.039 - 0.078: 329 0.078 - 0.116: 83 0.116 - 0.155: 14 0.155 - 0.194: 2 Chirality restraints: 1524 Sorted by residual: chirality pdb=" C4 LOP B 701 " pdb=" C3 LOP B 701 " pdb=" C5 LOP B 701 " pdb=" O5 LOP B 701 " both_signs ideal model delta sigma weight residual False -2.34 -2.53 0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" C4 LOP A 701 " pdb=" C3 LOP A 701 " pdb=" C5 LOP A 701 " pdb=" O5 LOP A 701 " both_signs ideal model delta sigma weight residual False -2.34 -2.53 0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CA PRO A 129 " pdb=" N PRO A 129 " pdb=" C PRO A 129 " pdb=" CB PRO A 129 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1521 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 128 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 129 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 128 " 0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO B 129 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 387 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 388 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " -0.016 5.00e-02 4.00e+02 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2334 2.79 - 3.32: 9964 3.32 - 3.84: 15480 3.84 - 4.37: 17627 4.37 - 4.90: 31523 Nonbonded interactions: 76928 Sorted by model distance: nonbonded pdb=" OD1 ASP A 499 " pdb=" N ILE A 500 " model vdw 2.258 2.520 nonbonded pdb=" OD1 ASP B 499 " pdb=" N ILE B 500 " model vdw 2.259 2.520 nonbonded pdb=" NZ LYS A 531 " pdb=" O ILE A 535 " model vdw 2.297 2.520 nonbonded pdb=" NZ LYS B 531 " pdb=" O ILE B 535 " model vdw 2.297 2.520 nonbonded pdb=" O THR A 273 " pdb=" OG1 THR A 277 " model vdw 2.311 2.440 ... (remaining 76923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=0.94 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 7.770 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.840 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 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 : 0.006 0.072 9788 Z= 0.415 Angle : 0.649 11.311 13226 Z= 0.342 Chirality : 0.040 0.194 1524 Planarity : 0.003 0.034 1664 Dihedral : 14.908 87.681 3630 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 0.00 % 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: -3.04 (0.22), residues: 1196 helix: -0.93 (0.17), residues: 778 sheet: -3.80 (0.67), residues: 56 loop : -4.02 (0.27), residues: 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2710 time to fit residues: 47.5039 Evaluate side-chains 97 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5556 ------------------------------------------------------------------------------- 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-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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: 62.1429 > 50: distance: 48 - 54: 15.705 distance: 54 - 55: 26.056 distance: 55 - 56: 21.341 distance: 55 - 58: 27.460 distance: 56 - 59: 14.934 distance: 59 - 60: 32.211 distance: 60 - 61: 9.366 distance: 60 - 63: 47.375 distance: 61 - 62: 25.185 distance: 61 - 67: 36.777 distance: 63 - 64: 61.775 distance: 64 - 65: 20.300 distance: 65 - 66: 25.912 distance: 67 - 68: 10.186 distance: 67 - 73: 17.247 distance: 68 - 69: 21.886 distance: 68 - 71: 22.558 distance: 69 - 70: 28.770 distance: 69 - 74: 10.921 distance: 71 - 72: 34.079 distance: 72 - 73: 10.817 distance: 74 - 75: 15.445 distance: 75 - 76: 30.433 distance: 76 - 77: 23.985 distance: 76 - 78: 11.366 distance: 79 - 80: 15.754 distance: 79 - 82: 16.323 distance: 80 - 81: 27.019 distance: 80 - 84: 4.768 distance: 82 - 83: 12.721 distance: 84 - 85: 11.975 distance: 85 - 86: 8.417 distance: 85 - 88: 24.334 distance: 86 - 87: 7.021 distance: 86 - 92: 21.391 distance: 87 - 124: 15.867 distance: 88 - 89: 4.818 distance: 89 - 90: 30.760 distance: 89 - 91: 29.144 distance: 92 - 93: 13.622 distance: 93 - 94: 18.376 distance: 93 - 96: 16.099 distance: 94 - 95: 21.870 distance: 94 - 104: 18.223 distance: 95 - 132: 15.084 distance: 96 - 97: 15.899 distance: 97 - 98: 7.970 distance: 97 - 99: 10.356 distance: 98 - 100: 12.009 distance: 99 - 101: 10.286 distance: 100 - 102: 6.489 distance: 101 - 102: 4.926 distance: 102 - 103: 9.208 distance: 104 - 105: 18.858 distance: 105 - 106: 14.091 distance: 105 - 108: 8.397 distance: 106 - 107: 15.595 distance: 106 - 115: 25.608 distance: 107 - 140: 15.082 distance: 108 - 109: 39.887 distance: 109 - 110: 22.378 distance: 110 - 111: 11.206 distance: 111 - 112: 7.058 distance: 112 - 113: 21.802 distance: 112 - 114: 18.878 distance: 115 - 116: 16.819 distance: 116 - 117: 18.939 distance: 116 - 119: 21.597 distance: 117 - 118: 22.997 distance: 117 - 124: 10.900 distance: 118 - 147: 11.246 distance: 119 - 120: 25.108 distance: 120 - 121: 19.329 distance: 121 - 122: 8.731 distance: 124 - 125: 10.433 distance: 125 - 126: 9.202 distance: 125 - 128: 13.885 distance: 126 - 127: 28.857 distance: 126 - 132: 9.738 distance: 127 - 154: 23.592 distance: 128 - 129: 7.036 distance: 129 - 130: 28.522 distance: 129 - 131: 24.209