Starting phenix.real_space_refine on Wed Mar 5 18:15:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qcz_18338/03_2025/8qcz_18338.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qcz_18338/03_2025/8qcz_18338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qcz_18338/03_2025/8qcz_18338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qcz_18338/03_2025/8qcz_18338.map" model { file = "/net/cci-nas-00/data/ceres_data/8qcz_18338/03_2025/8qcz_18338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qcz_18338/03_2025/8qcz_18338.cif" } resolution = 3.1 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= 0.004 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 19 5.16 5 C 2210 2.51 5 N 524 2.21 5 O 562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 3316 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3273 Classifications: {'peptide': 421} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 405} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.66, per 1000 atoms: 0.80 Number of scatterers: 3316 At special positions: 0 Unit cell: (80.352, 58.59, 64.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 19 16.00 O 562 8.00 N 524 7.00 C 2210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.86 Conformation dependent library (CDL) restraints added in 372.7 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 91.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 83 through 108 removed outlier: 3.689A pdb=" N ILE A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TYR A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLY A 106 " --> pdb=" O TRP A 102 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 108 " --> pdb=" O GLN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 4.150A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 149 removed outlier: 3.606A pdb=" N ILE A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TYR A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N MET A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 135 " --> pdb=" O MET A 131 " (cutoff:3.500A) Proline residue: A 136 - end of helix removed outlier: 5.115A pdb=" N LEU A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 149 through 170 removed outlier: 3.506A pdb=" N ILE A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 170 " --> pdb=" O TRP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 4.261A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 210 through 232 removed outlier: 3.585A pdb=" N ILE A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 242 through 272 removed outlier: 3.551A pdb=" N MET A 253 " --> pdb=" O HIS A 249 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 removed outlier: 3.714A pdb=" N ALA A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 307 Processing helix chain 'A' and resid 307 through 339 removed outlier: 4.750A pdb=" N ASN A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ARG A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 372 removed outlier: 4.033A pdb=" N VAL A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 357 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 396 Processing helix chain 'A' and resid 400 through 431 removed outlier: 3.591A pdb=" N VAL A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 419 " --> pdb=" O MET A 415 " (cutoff:3.500A) Proline residue: A 420 - end of helix Processing helix chain 'A' and resid 434 through 464 removed outlier: 3.576A pdb=" N LEU A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 486 removed outlier: 3.514A pdb=" N GLY A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 473 " --> pdb=" O GLY A 469 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 498 263 hydrogen bonds defined for protein. 789 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: 0.90 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 1319 1.38 - 1.55: 2051 1.55 - 1.72: 0 1.72 - 1.89: 31 1.89 - 2.06: 4 Bond restraints: 3405 Sorted by residual: bond pdb=" CG HIS A 338 " pdb=" CD2 HIS A 338 " ideal model delta sigma weight residual 1.354 1.325 0.029 1.10e-02 8.26e+03 7.02e+00 bond pdb=" N ARG A 348 " pdb=" CA ARG A 348 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.73e+00 bond pdb=" N LEU A 132 " pdb=" CA LEU A 132 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.33e-02 5.65e+03 5.72e+00 bond pdb=" N HIS A 338 " pdb=" CA HIS A 338 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.28e-02 6.10e+03 4.86e+00 bond pdb=" N LYS A 375 " pdb=" CA LYS A 375 " ideal model delta sigma weight residual 1.458 1.485 -0.026 1.26e-02 6.30e+03 4.42e+00 ... (remaining 3400 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 4502 1.52 - 3.04: 111 3.04 - 4.56: 26 4.56 - 6.08: 9 6.08 - 7.60: 3 Bond angle restraints: 4651 Sorted by residual: angle pdb=" C ALA A 120 " pdb=" N PHE A 121 " pdb=" CA PHE A 121 " ideal model delta sigma weight residual 120.29 115.19 5.10 1.42e+00 4.96e-01 1.29e+01 angle pdb=" N PHE A 121 " pdb=" CA PHE A 121 " pdb=" C PHE A 121 " ideal model delta sigma weight residual 111.36 107.51 3.85 1.09e+00 8.42e-01 1.25e+01 angle pdb=" N HIS A 338 " pdb=" CA HIS A 338 " pdb=" C HIS A 338 " ideal model delta sigma weight residual 113.88 109.85 4.03 1.23e+00 6.61e-01 1.08e+01 angle pdb=" N MET A 197 " pdb=" CA MET A 197 " pdb=" C MET A 197 " ideal model delta sigma weight residual 109.81 117.01 -7.20 2.21e+00 2.05e-01 1.06e+01 angle pdb=" CA LEU A 139 " pdb=" C LEU A 139 " pdb=" N PRO A 140 " ideal model delta sigma weight residual 120.77 123.84 -3.07 9.70e-01 1.06e+00 1.00e+01 ... (remaining 4646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 1694 16.03 - 32.05: 170 32.05 - 48.08: 57 48.08 - 64.11: 12 64.11 - 80.13: 5 Dihedral angle restraints: 1938 sinusoidal: 730 harmonic: 1208 Sorted by residual: dihedral pdb=" CA TYR A 94 " pdb=" C TYR A 94 " pdb=" N SER A 95 " pdb=" CA SER A 95 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" C2D HEM A 601 " pdb=" C3D HEM A 601 " pdb=" CAD HEM A 601 " pdb=" CBD HEM A 601 " ideal model delta sinusoidal sigma weight residual 0.00 78.36 -78.36 2 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" C1A HEM A 601 " pdb=" C2A HEM A 601 " pdb=" CAA HEM A 601 " pdb=" CBA HEM A 601 " ideal model delta sinusoidal sigma weight residual 180.00 103.37 76.63 2 2.00e+01 2.50e-03 1.14e+01 ... (remaining 1935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 367 0.032 - 0.064: 133 0.064 - 0.096: 30 0.096 - 0.128: 9 0.128 - 0.160: 3 Chirality restraints: 542 Sorted by residual: chirality pdb=" CA ARG A 370 " pdb=" N ARG A 370 " pdb=" C ARG A 370 " pdb=" CB ARG A 370 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA HIS A 338 " pdb=" N HIS A 338 " pdb=" C HIS A 338 " pdb=" CB HIS A 338 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA MET A 197 " pdb=" N MET A 197 " pdb=" C MET A 197 " pdb=" CB MET A 197 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 539 not shown) Planarity restraints: 559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 467 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 468 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 337 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C TRP A 337 " 0.028 2.00e-02 2.50e+03 pdb=" O TRP A 337 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS A 338 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 132 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C LEU A 132 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU A 132 " -0.010 2.00e-02 2.50e+03 pdb=" N THR A 133 " -0.010 2.00e-02 2.50e+03 ... (remaining 556 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 827 2.79 - 3.32: 3454 3.32 - 3.84: 5559 3.84 - 4.37: 6841 4.37 - 4.90: 11678 Nonbonded interactions: 28359 Sorted by model distance: nonbonded pdb=" N GLU A 274 " pdb=" OE1 GLU A 274 " model vdw 2.259 3.120 nonbonded pdb=" O LYS A 168 " pdb=" OG SER A 171 " model vdw 2.282 3.040 nonbonded pdb=" O TYR A 374 " pdb=" OG1 THR A 378 " model vdw 2.311 3.040 nonbonded pdb=" O ALA A 283 " pdb=" OH TYR A 431 " model vdw 2.320 3.040 nonbonded pdb=" O THR A 373 " pdb=" OG1 THR A 373 " model vdw 2.327 3.040 ... (remaining 28354 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.580 Find NCS groups from input model: 0.030 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 0.032 3405 Z= 0.241 Angle : 0.628 7.602 4651 Z= 0.349 Chirality : 0.038 0.160 542 Planarity : 0.004 0.050 559 Dihedral : 15.355 80.133 1168 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.21 (0.40), residues: 417 helix: 0.39 (0.26), residues: 351 sheet: None (None), residues: 0 loop : -0.56 (0.83), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 125 HIS 0.007 0.001 HIS A 338 PHE 0.007 0.001 PHE A 413 TYR 0.017 0.001 TYR A 392 ARG 0.001 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.358 Fit side-chains REVERT: A 194 ILE cc_start: 0.8108 (mm) cc_final: 0.7810 (mt) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1029 time to fit residues: 8.0688 Evaluate side-chains 55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.102586 restraints weight = 3945.604| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.47 r_work: 0.3129 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3405 Z= 0.235 Angle : 0.587 8.279 4651 Z= 0.297 Chirality : 0.040 0.143 542 Planarity : 0.004 0.038 559 Dihedral : 7.281 78.331 459 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.70 % Allowed : 14.20 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.50 (0.40), residues: 417 helix: 1.31 (0.26), residues: 358 sheet: None (None), residues: 0 loop : -0.61 (0.90), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 205 HIS 0.002 0.001 HIS A 338 PHE 0.013 0.001 PHE A 472 TYR 0.019 0.001 TYR A 94 ARG 0.001 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.349 Fit side-chains REVERT: A 191 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.6525 (tt0) REVERT: A 194 ILE cc_start: 0.8263 (mm) cc_final: 0.7973 (mt) REVERT: A 216 SER cc_start: 0.8264 (m) cc_final: 0.7964 (p) REVERT: A 230 PHE cc_start: 0.8254 (m-80) cc_final: 0.8011 (m-80) REVERT: A 456 SER cc_start: 0.8434 (t) cc_final: 0.8015 (p) outliers start: 6 outliers final: 2 residues processed: 66 average time/residue: 0.1192 time to fit residues: 10.2053 Evaluate side-chains 48 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104955 restraints weight = 3812.472| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.47 r_work: 0.3110 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3405 Z= 0.221 Angle : 0.557 8.193 4651 Z= 0.277 Chirality : 0.039 0.141 542 Planarity : 0.004 0.036 559 Dihedral : 7.260 78.282 459 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.27 % Allowed : 16.19 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.76 (0.40), residues: 417 helix: 1.49 (0.26), residues: 358 sheet: None (None), residues: 0 loop : -0.56 (0.90), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 205 HIS 0.002 0.001 HIS A 338 PHE 0.014 0.001 PHE A 472 TYR 0.022 0.001 TYR A 94 ARG 0.001 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.355 Fit side-chains REVERT: A 191 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.6510 (tt0) REVERT: A 216 SER cc_start: 0.8353 (m) cc_final: 0.8055 (p) REVERT: A 272 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7837 (t80) REVERT: A 456 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.7977 (p) outliers start: 8 outliers final: 3 residues processed: 61 average time/residue: 0.1067 time to fit residues: 8.7870 Evaluate side-chains 54 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 456 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.130164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107624 restraints weight = 3842.954| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.47 r_work: 0.3063 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3405 Z= 0.214 Angle : 0.555 8.372 4651 Z= 0.275 Chirality : 0.039 0.154 542 Planarity : 0.004 0.034 559 Dihedral : 7.231 78.202 459 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.84 % Allowed : 15.62 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.95 (0.40), residues: 417 helix: 1.65 (0.26), residues: 358 sheet: None (None), residues: 0 loop : -0.75 (0.86), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 205 HIS 0.001 0.000 HIS A 338 PHE 0.014 0.001 PHE A 472 TYR 0.021 0.001 TYR A 94 ARG 0.001 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.272 Fit side-chains REVERT: A 191 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6357 (tt0) REVERT: A 216 SER cc_start: 0.8332 (m) cc_final: 0.8010 (p) REVERT: A 272 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7806 (t80) REVERT: A 495 LYS cc_start: 0.7158 (mttt) cc_final: 0.6544 (pttm) outliers start: 10 outliers final: 6 residues processed: 59 average time/residue: 0.0902 time to fit residues: 7.3003 Evaluate side-chains 57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 456 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.105368 restraints weight = 3829.518| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.52 r_work: 0.3105 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3405 Z= 0.193 Angle : 0.532 7.869 4651 Z= 0.267 Chirality : 0.039 0.155 542 Planarity : 0.004 0.034 559 Dihedral : 7.174 78.021 459 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.98 % Allowed : 16.76 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.41), residues: 417 helix: 1.79 (0.26), residues: 359 sheet: None (None), residues: 0 loop : -0.52 (0.89), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 367 HIS 0.002 0.001 HIS A 338 PHE 0.014 0.001 PHE A 413 TYR 0.020 0.001 TYR A 94 ARG 0.001 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.328 Fit side-chains REVERT: A 191 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.6431 (tt0) REVERT: A 201 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7443 (mp) REVERT: A 216 SER cc_start: 0.8347 (m) cc_final: 0.8025 (p) REVERT: A 272 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7770 (t80) outliers start: 14 outliers final: 8 residues processed: 57 average time/residue: 0.1030 time to fit residues: 8.0215 Evaluate side-chains 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 456 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.0050 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.129523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.105886 restraints weight = 3851.872| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.54 r_work: 0.3109 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3405 Z= 0.194 Angle : 0.551 8.884 4651 Z= 0.271 Chirality : 0.038 0.155 542 Planarity : 0.004 0.034 559 Dihedral : 7.151 78.014 459 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.27 % Allowed : 20.17 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.41), residues: 417 helix: 1.84 (0.26), residues: 359 sheet: None (None), residues: 0 loop : -0.62 (0.88), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 205 HIS 0.002 0.001 HIS A 338 PHE 0.015 0.001 PHE A 413 TYR 0.020 0.001 TYR A 94 ARG 0.001 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.350 Fit side-chains REVERT: A 191 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6441 (tt0) REVERT: A 201 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7426 (mp) REVERT: A 216 SER cc_start: 0.8350 (m) cc_final: 0.8014 (p) REVERT: A 272 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7767 (t80) REVERT: A 495 LYS cc_start: 0.7074 (mttt) cc_final: 0.6494 (pttm) outliers start: 8 outliers final: 4 residues processed: 57 average time/residue: 0.1024 time to fit residues: 8.0849 Evaluate side-chains 57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 54.8365 > 50: distance: 86 - 104: 32.996 distance: 91 - 112: 9.384 distance: 95 - 100: 9.357 distance: 96 - 120: 10.872 distance: 100 - 101: 17.956 distance: 101 - 102: 20.775 distance: 102 - 103: 31.243 distance: 102 - 104: 26.741 distance: 104 - 105: 33.680 distance: 105 - 106: 35.283 distance: 105 - 108: 44.651 distance: 106 - 107: 7.026 distance: 106 - 112: 13.704 distance: 107 - 139: 27.731 distance: 108 - 109: 24.515 distance: 109 - 110: 30.650 distance: 109 - 111: 27.292 distance: 112 - 113: 10.886 distance: 113 - 114: 15.864 distance: 113 - 116: 7.203 distance: 114 - 115: 12.625 distance: 114 - 120: 10.143 distance: 115 - 145: 19.564 distance: 116 - 117: 13.736 distance: 116 - 118: 29.637 distance: 117 - 119: 16.914 distance: 120 - 121: 15.352 distance: 121 - 122: 21.765 distance: 121 - 124: 20.853 distance: 122 - 123: 8.272 distance: 122 - 131: 15.154 distance: 123 - 152: 25.743 distance: 124 - 125: 26.110 distance: 125 - 126: 29.048 distance: 125 - 127: 19.761 distance: 126 - 128: 16.205 distance: 127 - 129: 12.629 distance: 128 - 130: 13.906 distance: 129 - 130: 11.258 distance: 131 - 132: 22.179 distance: 132 - 133: 12.002 distance: 132 - 135: 10.372 distance: 133 - 134: 21.007 distance: 133 - 139: 16.863 distance: 134 - 163: 11.557 distance: 135 - 136: 14.658 distance: 136 - 137: 10.783 distance: 136 - 138: 16.199 distance: 139 - 140: 18.307 distance: 140 - 141: 8.821 distance: 140 - 143: 34.127 distance: 141 - 142: 31.812 distance: 141 - 145: 23.413 distance: 142 - 171: 43.907 distance: 143 - 144: 23.956 distance: 145 - 146: 29.005 distance: 146 - 147: 30.573 distance: 146 - 149: 21.980 distance: 147 - 148: 38.397 distance: 147 - 152: 15.516 distance: 148 - 178: 26.004 distance: 149 - 150: 19.459 distance: 149 - 151: 37.722 distance: 152 - 153: 27.751 distance: 153 - 154: 15.172 distance: 153 - 156: 31.722 distance: 154 - 155: 43.904 distance: 154 - 163: 21.711 distance: 155 - 185: 19.614 distance: 156 - 157: 14.747 distance: 157 - 158: 20.132 distance: 157 - 159: 21.599 distance: 158 - 160: 17.911 distance: 159 - 161: 8.866 distance: 160 - 162: 9.385 distance: 161 - 162: 28.671 distance: 163 - 164: 14.028 distance: 164 - 165: 10.425 distance: 164 - 167: 17.552 distance: 165 - 166: 17.103 distance: 165 - 171: 26.606 distance: 166 - 189: 15.766 distance: 167 - 168: 20.286 distance: 168 - 170: 16.818 distance: 171 - 172: 10.869 distance: 172 - 173: 3.220 distance: 172 - 175: 12.634 distance: 173 - 178: 8.568 distance: 174 - 194: 10.347 distance: 175 - 176: 11.803 distance: 175 - 177: 16.571