Starting phenix.real_space_refine on Fri Jan 17 01:29:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c4o_45192/01_2025/9c4o_45192_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c4o_45192/01_2025/9c4o_45192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c4o_45192/01_2025/9c4o_45192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c4o_45192/01_2025/9c4o_45192.map" model { file = "/net/cci-nas-00/data/ceres_data/9c4o_45192/01_2025/9c4o_45192_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c4o_45192/01_2025/9c4o_45192_trim.cif" } resolution = 1.99 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= 0.064 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 19 5.16 5 C 3205 2.51 5 N 915 2.21 5 O 1143 1.98 5 H 4883 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10166 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 10030 Classifications: {'peptide': 661} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 633} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 136 Unusual residues: {' CA': 1, 'PQQ': 1} Classifications: {'undetermined': 2, 'water': 111} Link IDs: {None: 112} Time building chain proxies: 5.51, per 1000 atoms: 0.54 Number of scatterers: 10166 At special positions: 0 Unit cell: (86.92, 62.32, 72.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 19 16.00 O 1143 8.00 N 915 7.00 C 3205 6.00 H 4883 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 585 " 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 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 749.2 milliseconds 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1178 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 6 sheets defined 6.5% alpha, 53.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.987A pdb=" N THR A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 264 through 271 Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.861A pdb=" N GLN A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 4.264A pdb=" N TYR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51 removed outlier: 4.284A pdb=" N ALA A 46 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN A 132 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG A 105 " --> pdb=" O MET A 152 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL A 154 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR A 107 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N THR A 156 " --> pdb=" O TYR A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 77 Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 172 removed outlier: 4.451A pdb=" N TRP A 405 " --> pdb=" O PRO A 349 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR A 351 " --> pdb=" O THR A 403 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR A 403 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR A 353 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 401 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY A 355 " --> pdb=" O PRO A 399 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASN A 357 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 397 " --> pdb=" O ASN A 357 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TRP A 395 " --> pdb=" O GLU A 359 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N MET A 361 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU A 393 " --> pdb=" O MET A 361 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU A 363 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG A 391 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG A 365 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP A 389 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLY A 367 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N TRP A 447 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N PHE A 471 " --> pdb=" O TRP A 447 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU A 513 " --> pdb=" O GLN A 556 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLN A 556 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER A 515 " --> pdb=" O TRP A 554 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TRP A 554 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ALA A 517 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU A 552 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE A 519 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ALA A 550 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR A 521 " --> pdb=" O GLN A 548 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLN A 548 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR A 523 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ARG A 546 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASP A 525 " --> pdb=" O LYS A 544 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LYS A 544 " --> pdb=" O ASP A 525 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE A 527 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA A 542 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL A 529 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LYS A 540 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 373 Processing sheet with id=AA5, first strand: chain 'A' and resid 622 through 623 Processing sheet with id=AA6, first strand: chain 'A' and resid 668 through 671 removed outlier: 3.561A pdb=" N SER A 670 " --> pdb=" O GLU A 682 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 795 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: 4.10 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4883 1.03 - 1.23: 15 1.23 - 1.42: 2322 1.42 - 1.62: 2914 1.62 - 1.81: 36 Bond restraints: 10170 Sorted by residual: bond pdb=" C PRO A 683 " pdb=" N SER A 684 " ideal model delta sigma weight residual 1.327 1.308 0.018 1.71e-02 3.42e+03 1.16e+00 bond pdb=" CA LYS A 277 " pdb=" C LYS A 277 " ideal model delta sigma weight residual 1.526 1.515 0.011 1.08e-02 8.57e+03 1.03e+00 bond pdb=" C ALA A 450 " pdb=" N GLY A 451 " ideal model delta sigma weight residual 1.330 1.317 0.013 1.32e-02 5.74e+03 9.14e-01 bond pdb=" C GLU A 363 " pdb=" N ASN A 364 " ideal model delta sigma weight residual 1.331 1.318 0.013 1.40e-02 5.10e+03 8.48e-01 bond pdb=" C ARG A 589 " pdb=" N MET A 590 " ideal model delta sigma weight residual 1.326 1.309 0.017 1.84e-02 2.95e+03 8.42e-01 ... (remaining 10165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 17527 1.29 - 2.58: 613 2.58 - 3.88: 50 3.88 - 5.17: 12 5.17 - 6.46: 2 Bond angle restraints: 18204 Sorted by residual: angle pdb=" N GLY A 492 " pdb=" CA GLY A 492 " pdb=" C GLY A 492 " ideal model delta sigma weight residual 114.67 111.15 3.52 1.10e+00 8.26e-01 1.02e+01 angle pdb=" N ASP A 530 " pdb=" CA ASP A 530 " pdb=" C ASP A 530 " ideal model delta sigma weight residual 111.24 108.22 3.02 1.29e+00 6.01e-01 5.48e+00 angle pdb=" N SER A 375 " pdb=" CA SER A 375 " pdb=" C SER A 375 " ideal model delta sigma weight residual 112.12 108.99 3.13 1.34e+00 5.57e-01 5.46e+00 angle pdb=" N PRO A 685 " pdb=" CA PRO A 685 " pdb=" C PRO A 685 " ideal model delta sigma weight residual 112.47 116.85 -4.38 2.06e+00 2.36e-01 4.52e+00 angle pdb=" CA VAL A 348 " pdb=" C VAL A 348 " pdb=" N PRO A 349 " ideal model delta sigma weight residual 117.33 119.30 -1.97 1.01e+00 9.80e-01 3.82e+00 ... (remaining 18199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4301 17.76 - 35.52: 360 35.52 - 53.28: 114 53.28 - 71.04: 37 71.04 - 88.80: 16 Dihedral angle restraints: 4828 sinusoidal: 2618 harmonic: 2210 Sorted by residual: dihedral pdb=" CA TYR A 680 " pdb=" C TYR A 680 " pdb=" N TYR A 681 " pdb=" CA TYR A 681 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA PRO A 685 " pdb=" C PRO A 685 " pdb=" N GLY A 686 " pdb=" CA GLY A 686 " ideal model delta harmonic sigma weight residual -180.00 -155.22 -24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ASP A 398 " pdb=" C ASP A 398 " pdb=" N PRO A 399 " pdb=" CA PRO A 399 " ideal model delta harmonic sigma weight residual 180.00 155.87 24.13 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 4825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 454 0.034 - 0.068: 216 0.068 - 0.102: 45 0.102 - 0.137: 29 0.137 - 0.171: 1 Chirality restraints: 745 Sorted by residual: chirality pdb=" CA PRO A 685 " pdb=" N PRO A 685 " pdb=" C PRO A 685 " pdb=" CB PRO A 685 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA ILE A 501 " pdb=" N ILE A 501 " pdb=" C ILE A 501 " pdb=" CB ILE A 501 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE A 104 " pdb=" N ILE A 104 " pdb=" C ILE A 104 " pdb=" CB ILE A 104 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 742 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 684 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 685 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 685 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 685 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 91 " 0.114 9.50e-02 1.11e+02 3.82e-02 1.62e+00 pdb=" NE ARG A 91 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 91 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 91 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 91 " 0.004 2.00e-02 2.50e+03 pdb="HH11 ARG A 91 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 91 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 91 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 91 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 192 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 193 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " -0.017 5.00e-02 4.00e+02 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 714 2.18 - 2.79: 21047 2.79 - 3.39: 30425 3.39 - 4.00: 43620 4.00 - 4.60: 63096 Nonbonded interactions: 158902 Sorted by model distance: nonbonded pdb=" O LEU A 479 " pdb=" H ASN A 490 " model vdw 1.575 2.450 nonbonded pdb=" HH TYR A 481 " pdb=" O2B PQQ A 802 " model vdw 1.583 2.450 nonbonded pdb=" HH TYR A 464 " pdb=" OE2 GLU A 502 " model vdw 1.607 2.450 nonbonded pdb=" O VAL A 638 " pdb=" H LEU A 662 " model vdw 1.616 2.450 nonbonded pdb="HD21 ASN A 357 " pdb=" OE2 GLU A 359 " model vdw 1.627 2.450 ... (remaining 158897 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=1.00 max=1.00 mean=1.00 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: 2.290 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: 0.210 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.500 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 0.037 5287 Z= 0.277 Angle : 0.647 6.461 7177 Z= 0.367 Chirality : 0.044 0.171 745 Planarity : 0.005 0.051 958 Dihedral : 16.532 88.799 1925 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.18 % Allowed : 14.76 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.32), residues: 659 helix: -1.84 (0.64), residues: 47 sheet: 0.18 (0.25), residues: 349 loop : 0.34 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.002 0.001 HIS A 445 PHE 0.016 0.002 PHE A 352 TYR 0.017 0.002 TYR A 681 ARG 0.004 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8545 (mmp) cc_final: 0.8331 (mmp) outliers start: 1 outliers final: 1 residues processed: 87 average time/residue: 2.7302 time to fit residues: 247.5696 Evaluate side-chains 84 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.150336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.137134 restraints weight = 11566.983| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 0.99 r_work: 0.3602 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5287 Z= 0.238 Angle : 0.580 6.422 7177 Z= 0.317 Chirality : 0.044 0.169 745 Planarity : 0.005 0.042 958 Dihedral : 6.778 74.239 746 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.11 % Allowed : 13.84 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.32), residues: 659 helix: -1.82 (0.65), residues: 47 sheet: -0.01 (0.25), residues: 351 loop : 0.56 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.001 0.001 HIS A 649 PHE 0.017 0.002 PHE A 352 TYR 0.017 0.001 TYR A 681 ARG 0.005 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8561 (mmp) cc_final: 0.8123 (mmp) REVERT: A 377 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6537 (mpt) REVERT: A 379 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6797 (tm-30) REVERT: A 576 ARG cc_start: 0.7634 (mmp-170) cc_final: 0.7299 (mmp-170) REVERT: A 595 ARG cc_start: 0.7735 (mtm180) cc_final: 0.7399 (ttp-170) outliers start: 6 outliers final: 2 residues processed: 91 average time/residue: 2.6452 time to fit residues: 251.2590 Evaluate side-chains 86 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 54 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.148673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.135326 restraints weight = 11654.911| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 0.99 r_work: 0.3577 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5287 Z= 0.275 Angle : 0.593 5.973 7177 Z= 0.325 Chirality : 0.044 0.176 745 Planarity : 0.005 0.040 958 Dihedral : 6.884 74.796 746 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.48 % Allowed : 13.47 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.32), residues: 659 helix: -1.78 (0.64), residues: 47 sheet: 0.05 (0.25), residues: 350 loop : 0.50 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 568 HIS 0.002 0.001 HIS A 213 PHE 0.017 0.002 PHE A 352 TYR 0.017 0.002 TYR A 681 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8617 (mmp) cc_final: 0.8206 (mmp) REVERT: A 377 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6518 (mpt) REVERT: A 394 MET cc_start: 0.8560 (ttt) cc_final: 0.8310 (ttt) REVERT: A 595 ARG cc_start: 0.7713 (mtm180) cc_final: 0.7386 (ttp-170) outliers start: 8 outliers final: 3 residues processed: 88 average time/residue: 2.6322 time to fit residues: 242.2707 Evaluate side-chains 86 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.1980 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.0870 chunk 43 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.150160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.136990 restraints weight = 11580.426| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 0.98 r_work: 0.3597 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5287 Z= 0.239 Angle : 0.570 6.593 7177 Z= 0.310 Chirality : 0.044 0.167 745 Planarity : 0.004 0.037 958 Dihedral : 6.787 74.525 746 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.29 % Allowed : 13.84 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.32), residues: 659 helix: -1.64 (0.64), residues: 47 sheet: -0.03 (0.25), residues: 350 loop : 0.53 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.002 0.001 HIS A 213 PHE 0.016 0.002 PHE A 352 TYR 0.016 0.001 TYR A 681 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8556 (mmp) cc_final: 0.8156 (mmp) REVERT: A 364 ASN cc_start: 0.7751 (m110) cc_final: 0.7491 (t0) REVERT: A 377 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6454 (mpt) REVERT: A 394 MET cc_start: 0.8516 (ttt) cc_final: 0.8258 (ttt) REVERT: A 595 ARG cc_start: 0.7671 (mtm180) cc_final: 0.7327 (ttp-170) outliers start: 7 outliers final: 3 residues processed: 90 average time/residue: 2.4928 time to fit residues: 234.8382 Evaluate side-chains 81 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN A 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.145327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.131867 restraints weight = 11654.398| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 0.99 r_work: 0.3533 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 5287 Z= 0.391 Angle : 0.668 7.324 7177 Z= 0.368 Chirality : 0.044 0.203 745 Planarity : 0.006 0.047 958 Dihedral : 7.288 75.707 746 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.11 % Allowed : 14.02 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.32), residues: 659 helix: -1.81 (0.61), residues: 47 sheet: 0.27 (0.26), residues: 345 loop : 0.40 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 568 HIS 0.003 0.001 HIS A 445 PHE 0.019 0.003 PHE A 352 TYR 0.018 0.002 TYR A 681 ARG 0.003 0.001 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8638 (mmp) cc_final: 0.8191 (mmp) REVERT: A 377 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6393 (mpt) REVERT: A 595 ARG cc_start: 0.7730 (mtm180) cc_final: 0.7392 (ttp-170) outliers start: 6 outliers final: 3 residues processed: 83 average time/residue: 2.7887 time to fit residues: 241.2016 Evaluate side-chains 83 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.0912 > 50: distance: 129 - 130: 4.412 distance: 130 - 131: 5.998 distance: 130 - 133: 6.419 distance: 130 - 138: 4.081 distance: 131 - 132: 5.633 distance: 131 - 141: 5.757 distance: 133 - 134: 3.926 distance: 133 - 139: 3.374 distance: 133 - 140: 4.994 distance: 134 - 135: 4.578 distance: 134 - 136: 3.821 distance: 141 - 142: 8.824 distance: 141 - 151: 9.330 distance: 142 - 143: 10.125 distance: 142 - 145: 4.711 distance: 142 - 152: 6.183 distance: 143 - 144: 21.529 distance: 143 - 158: 11.474 distance: 145 - 146: 8.251 distance: 145 - 153: 3.173 distance: 146 - 147: 5.018 distance: 146 - 148: 4.487 distance: 147 - 149: 6.219 distance: 148 - 150: 6.342 distance: 148 - 156: 4.210 distance: 149 - 150: 3.897 distance: 149 - 157: 3.978 distance: 158 - 159: 6.155 distance: 158 - 170: 17.782 distance: 159 - 160: 4.600 distance: 159 - 171: 4.711 distance: 160 - 161: 6.536 distance: 162 - 163: 4.345 distance: 162 - 172: 3.550 distance: 162 - 173: 4.239 distance: 163 - 164: 3.706 distance: 163 - 165: 3.102 distance: 165 - 175: 3.540 distance: 166 - 168: 3.710 distance: 166 - 176: 3.339 distance: 167 - 168: 3.722 distance: 167 - 177: 3.202 distance: 169 - 178: 3.482 distance: 179 - 186: 4.192 distance: 180 - 181: 5.359 distance: 180 - 183: 3.715 distance: 181 - 182: 5.195 distance: 181 - 195: 3.019 distance: 183 - 185: 3.281 distance: 183 - 188: 3.315 distance: 184 - 189: 6.583 distance: 184 - 190: 6.889 distance: 184 - 191: 5.770 distance: 195 - 202: 4.023 distance: 196 - 197: 5.582 distance: 196 - 199: 3.893 distance: 196 - 203: 4.006 distance: 197 - 198: 7.714 distance: 197 - 209: 6.626 distance: 199 - 204: 4.705 distance: 200 - 205: 3.589 distance: 201 - 206: 3.370 distance: 209 - 210: 3.602 distance: 209 - 215: 5.268 distance: 210 - 211: 5.937 distance: 210 - 213: 4.463 distance: 210 - 216: 4.112 distance: 211 - 212: 7.415 distance: 213 - 214: 10.760 distance: 213 - 217: 8.145 distance: 214 - 215: 10.503 distance: 214 - 220: 5.678 distance: 215 - 221: 3.124 distance: 215 - 222: 15.076 distance: 223 - 224: 4.852 distance: 224 - 225: 4.002 distance: 224 - 228: 7.525 distance: 224 - 229: 6.150 distance: 225 - 226: 3.026 distance: 225 - 230: 6.885 distance: 230 - 231: 4.368 distance: 230 - 238: 4.573 distance: 232 - 233: 6.548 distance: 232 - 244: 4.609 distance: 234 - 235: 3.041 distance: 235 - 236: 3.014 distance: 237 - 242: 3.337 distance: 244 - 245: 3.850 distance: 245 - 246: 4.755 distance: 245 - 249: 5.877 distance: 245 - 250: 4.719 distance: 246 - 247: 3.249 distance: 251 - 259: 3.009 distance: 252 - 253: 3.110 distance: 252 - 255: 4.378 distance: 253 - 254: 3.322 distance: 255 - 256: 5.368 distance: 255 - 262: 4.645 distance: 256 - 257: 4.213 distance: 256 - 258: 7.869