Starting phenix.real_space_refine on Thu Mar 6 03:20:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dad_27270/03_2025/8dad_27270.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dad_27270/03_2025/8dad_27270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dad_27270/03_2025/8dad_27270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dad_27270/03_2025/8dad_27270.map" model { file = "/net/cci-nas-00/data/ceres_data/8dad_27270/03_2025/8dad_27270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dad_27270/03_2025/8dad_27270.cif" } resolution = 3.85 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= -0.001 sd= 0.044 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 1656 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 19 5.16 5 C 2068 2.51 5 N 558 2.21 5 O 610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3255 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1428 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 55 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.89, per 1000 atoms: 0.89 Number of scatterers: 3255 At special positions: 0 Unit cell: (62.83, 64.89, 101.97, 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 19 16.00 O 610 8.00 N 558 7.00 C 2068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 1 " - " ASN B 343 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 399.5 milliseconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 12.0% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.898A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.194A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.215A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.585A pdb=" N MET H 112 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.638A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 121 hydrogen bonds defined for protein. 285 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: 0.86 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1052 1.34 - 1.46: 889 1.46 - 1.58: 1371 1.58 - 1.70: 0 1.70 - 1.83: 24 Bond restraints: 3336 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.94e+00 bond pdb=" C1 NAG J 1 " pdb=" C2 NAG J 1 " ideal model delta sigma weight residual 1.532 1.506 0.026 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C5 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.413 1.439 -0.026 2.00e-02 2.50e+03 1.72e+00 ... (remaining 3331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 4452 2.54 - 5.09: 78 5.09 - 7.63: 11 7.63 - 10.17: 1 10.17 - 12.72: 2 Bond angle restraints: 4544 Sorted by residual: angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 107.69 120.41 -12.72 2.01e+00 2.48e-01 4.00e+01 angle pdb=" N LEU B 390 " pdb=" CA LEU B 390 " pdb=" C LEU B 390 " ideal model delta sigma weight residual 109.76 115.86 -6.10 1.59e+00 3.96e-01 1.47e+01 angle pdb=" CA CYS B 391 " pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 114.40 122.98 -8.58 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CB MET H 118 " pdb=" CG MET H 118 " pdb=" SD MET H 118 " ideal model delta sigma weight residual 112.70 123.10 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " ideal model delta sigma weight residual 114.40 121.52 -7.12 2.30e+00 1.89e-01 9.57e+00 ... (remaining 4539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.03: 1767 20.03 - 40.07: 195 40.07 - 60.10: 38 60.10 - 80.13: 7 80.13 - 100.17: 10 Dihedral angle restraints: 2017 sinusoidal: 791 harmonic: 1226 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -166.15 80.15 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 19.42 73.58 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 164.39 -71.39 1 1.00e+01 1.00e-02 6.54e+01 ... (remaining 2014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 477 0.106 - 0.212: 23 0.212 - 0.318: 0 0.318 - 0.424: 0 0.424 - 0.529: 1 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA CYS B 391 " pdb=" N CYS B 391 " pdb=" C CYS B 391 " pdb=" CB CYS B 391 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" C4 NAG J 1 " pdb=" C3 NAG J 1 " pdb=" C5 NAG J 1 " pdb=" O4 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.34 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 7.44e-01 ... (remaining 498 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 36 " -0.012 2.00e-02 2.50e+03 1.85e-02 8.60e+00 pdb=" CG TRP L 36 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP L 36 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP L 36 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP L 36 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP L 36 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP L 36 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 36 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 36 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 36 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY H 8 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.61e+00 pdb=" N PRO H 9 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO H 9 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 9 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 527 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.022 5.00e-02 4.00e+02 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 631 2.77 - 3.30: 3114 3.30 - 3.84: 5612 3.84 - 4.37: 6247 4.37 - 4.90: 10905 Nonbonded interactions: 26509 Sorted by model distance: nonbonded pdb=" N GLU H 66 " pdb=" OE1 GLU H 66 " model vdw 2.238 3.120 nonbonded pdb=" OH TYR L 37 " pdb=" OE1 GLN L 90 " model vdw 2.287 3.040 nonbonded pdb=" O THR H 104 " pdb=" OH TYR B 473 " model vdw 2.293 3.040 nonbonded pdb=" OD2 ASP H 108 " pdb=" NH1 ARG L 54 " model vdw 2.310 3.120 nonbonded pdb=" N GLN H 65 " pdb=" OE1 GLN H 65 " model vdw 2.317 3.120 ... (remaining 26504 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.200 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3336 Z= 0.279 Angle : 0.832 12.716 4544 Z= 0.428 Chirality : 0.054 0.529 501 Planarity : 0.006 0.054 588 Dihedral : 17.766 100.167 1216 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.63 % Allowed : 26.98 % Favored : 72.38 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 9.52 % 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: -0.96 (0.42), residues: 418 helix: -2.01 (0.96), residues: 33 sheet: -0.55 (0.44), residues: 146 loop : -0.37 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP L 36 PHE 0.013 0.002 PHE H 27 TYR 0.009 0.001 TYR L 92 ARG 0.004 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 424 LYS cc_start: 0.8407 (ttpp) cc_final: 0.8126 (ttpp) outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 0.2213 time to fit residues: 20.2402 Evaluate side-chains 72 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.111933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.092636 restraints weight = 8741.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.095216 restraints weight = 5927.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.097201 restraints weight = 4526.031| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3336 Z= 0.223 Angle : 0.667 7.026 4544 Z= 0.337 Chirality : 0.046 0.146 501 Planarity : 0.005 0.050 588 Dihedral : 10.788 74.535 556 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.49 % Allowed : 24.76 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.94 (0.42), residues: 418 helix: -2.01 (0.98), residues: 34 sheet: -0.73 (0.41), residues: 158 loop : -0.15 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP L 36 PHE 0.037 0.002 PHE B 392 TYR 0.009 0.001 TYR L 92 ARG 0.003 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.8089 (t60) cc_final: 0.7676 (t60) REVERT: H 112 MET cc_start: 0.8252 (mpp) cc_final: 0.7053 (mpp) REVERT: L 78 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7841 (tmm160) REVERT: L 80 GLU cc_start: 0.7424 (tt0) cc_final: 0.7159 (tt0) outliers start: 11 outliers final: 6 residues processed: 84 average time/residue: 0.2036 time to fit residues: 20.0465 Evaluate side-chains 74 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.112278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.093363 restraints weight = 8667.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.095926 restraints weight = 5965.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.097837 restraints weight = 4568.951| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3336 Z= 0.213 Angle : 0.680 10.451 4544 Z= 0.338 Chirality : 0.046 0.177 501 Planarity : 0.005 0.047 588 Dihedral : 9.904 66.801 556 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.71 % Allowed : 24.44 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.91 (0.42), residues: 418 helix: -2.28 (0.92), residues: 33 sheet: -0.75 (0.40), residues: 157 loop : -0.06 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 36 PHE 0.027 0.002 PHE B 392 TYR 0.010 0.001 TYR L 92 ARG 0.004 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.8191 (t60) cc_final: 0.7717 (t60) REVERT: L 17 GLU cc_start: 0.7235 (pm20) cc_final: 0.6427 (pm20) REVERT: L 78 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7815 (tmm160) REVERT: L 80 GLU cc_start: 0.7438 (tt0) cc_final: 0.7016 (tt0) REVERT: L 83 ASP cc_start: 0.8023 (m-30) cc_final: 0.7790 (m-30) outliers start: 18 outliers final: 10 residues processed: 85 average time/residue: 0.1812 time to fit residues: 18.1607 Evaluate side-chains 76 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.110920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.092798 restraints weight = 8734.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.095212 restraints weight = 6110.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.096994 restraints weight = 4719.476| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3336 Z= 0.248 Angle : 0.641 7.526 4544 Z= 0.323 Chirality : 0.046 0.210 501 Planarity : 0.005 0.047 588 Dihedral : 9.095 60.130 556 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 6.03 % Allowed : 23.17 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.88 (0.42), residues: 418 helix: -2.33 (0.90), residues: 33 sheet: -0.72 (0.40), residues: 160 loop : -0.02 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 36 PHE 0.026 0.002 PHE B 392 TYR 0.009 0.001 TYR L 92 ARG 0.003 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.6674 (pm20) cc_final: 0.6401 (pm20) REVERT: H 47 TRP cc_start: 0.8302 (t60) cc_final: 0.7777 (t60) REVERT: H 72 ARG cc_start: 0.7884 (pmt-80) cc_final: 0.7606 (pmt-80) REVERT: H 112 MET cc_start: 0.8362 (mpp) cc_final: 0.7916 (mpp) REVERT: L 17 GLU cc_start: 0.7175 (pm20) cc_final: 0.6363 (pm20) REVERT: L 37 TYR cc_start: 0.8539 (m-80) cc_final: 0.8335 (m-80) outliers start: 19 outliers final: 15 residues processed: 85 average time/residue: 0.1791 time to fit residues: 18.0957 Evaluate side-chains 81 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.113024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.094659 restraints weight = 8727.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.097344 restraints weight = 5835.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.099301 restraints weight = 4373.621| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3336 Z= 0.186 Angle : 0.662 8.353 4544 Z= 0.327 Chirality : 0.045 0.129 501 Planarity : 0.005 0.046 588 Dihedral : 8.359 55.006 556 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 6.03 % Allowed : 22.54 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.74 (0.42), residues: 418 helix: -2.44 (0.87), residues: 33 sheet: -0.58 (0.40), residues: 155 loop : 0.06 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 36 PHE 0.017 0.002 PHE B 392 TYR 0.009 0.001 TYR L 88 ARG 0.005 0.001 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.6724 (pm20) cc_final: 0.6439 (pm20) REVERT: H 47 TRP cc_start: 0.8221 (t60) cc_final: 0.8009 (t60) REVERT: H 72 ARG cc_start: 0.8023 (pmt-80) cc_final: 0.7634 (pmt-80) REVERT: H 80 TYR cc_start: 0.8309 (m-10) cc_final: 0.8098 (m-10) REVERT: H 112 MET cc_start: 0.8338 (mpp) cc_final: 0.7868 (mpp) REVERT: L 11 LEU cc_start: 0.8299 (mm) cc_final: 0.8061 (mm) REVERT: L 17 GLU cc_start: 0.7350 (pm20) cc_final: 0.6581 (pm20) REVERT: L 37 TYR cc_start: 0.8705 (m-80) cc_final: 0.8490 (m-80) REVERT: L 101 GLN cc_start: 0.8044 (pm20) cc_final: 0.7573 (pm20) outliers start: 19 outliers final: 15 residues processed: 86 average time/residue: 0.1643 time to fit residues: 16.8618 Evaluate side-chains 86 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.8242 > 50: distance: 33 - 192: 33.894 distance: 36 - 189: 6.954 distance: 44 - 177: 31.215 distance: 47 - 174: 11.291 distance: 56 - 158: 32.327 distance: 59 - 155: 9.220 distance: 110 - 185: 25.327 distance: 113 - 182: 14.235 distance: 120 - 169: 32.989 distance: 123 - 166: 6.475 distance: 142 - 147: 9.436 distance: 147 - 148: 5.780 distance: 148 - 149: 9.687 distance: 148 - 151: 9.035 distance: 149 - 150: 14.340 distance: 149 - 155: 13.525 distance: 151 - 152: 9.158 distance: 152 - 154: 3.282 distance: 155 - 156: 8.684 distance: 156 - 157: 18.813 distance: 156 - 159: 21.171 distance: 157 - 158: 12.790 distance: 157 - 166: 28.222 distance: 159 - 160: 6.771 distance: 160 - 161: 11.300 distance: 160 - 162: 13.200 distance: 161 - 163: 10.691 distance: 162 - 164: 9.288 distance: 163 - 165: 13.138 distance: 164 - 165: 11.668 distance: 166 - 167: 8.554 distance: 167 - 168: 25.456 distance: 167 - 170: 12.268 distance: 168 - 169: 16.036 distance: 168 - 174: 34.031 distance: 170 - 171: 20.060 distance: 170 - 172: 30.971 distance: 171 - 173: 8.422 distance: 174 - 175: 9.635 distance: 175 - 176: 8.723 distance: 175 - 178: 13.412 distance: 176 - 177: 17.173 distance: 176 - 182: 11.312 distance: 178 - 179: 33.102 distance: 179 - 180: 24.471 distance: 179 - 181: 20.484 distance: 182 - 183: 4.089 distance: 183 - 184: 5.473 distance: 183 - 186: 6.244 distance: 184 - 185: 8.508 distance: 184 - 189: 14.271 distance: 186 - 187: 12.662 distance: 186 - 188: 18.743 distance: 189 - 190: 11.627 distance: 190 - 191: 19.272 distance: 190 - 193: 7.787 distance: 191 - 192: 23.831 distance: 191 - 197: 34.060 distance: 193 - 194: 13.480 distance: 193 - 195: 4.383 distance: 194 - 196: 14.949 distance: 197 - 198: 9.095 distance: 198 - 199: 13.117 distance: 198 - 201: 10.528 distance: 199 - 200: 25.690 distance: 199 - 203: 16.266 distance: 201 - 202: 5.346 distance: 203 - 204: 15.811 distance: 204 - 205: 36.613 distance: 204 - 207: 14.704 distance: 205 - 206: 26.096 distance: 205 - 214: 11.062 distance: 207 - 208: 11.907 distance: 208 - 209: 29.458 distance: 209 - 210: 4.306 distance: 210 - 211: 20.991 distance: 211 - 212: 7.651 distance: 211 - 213: 4.326 distance: 214 - 215: 22.614 distance: 215 - 216: 16.415 distance: 215 - 218: 26.778 distance: 216 - 217: 39.758 distance: 216 - 222: 9.394 distance: 218 - 219: 34.767 distance: 219 - 220: 12.446 distance: 219 - 221: 6.358 distance: 222 - 223: 11.940 distance: 223 - 224: 22.116 distance: 223 - 226: 21.529 distance: 224 - 225: 32.266 distance: 224 - 231: 16.154 distance: 225 - 247: 35.263 distance: 226 - 227: 35.354 distance: 227 - 228: 13.235 distance: 228 - 229: 13.058 distance: 228 - 230: 14.800