Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 16:34:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dly_27520/07_2023/8dly_27520.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dly_27520/07_2023/8dly_27520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dly_27520/07_2023/8dly_27520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dly_27520/07_2023/8dly_27520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dly_27520/07_2023/8dly_27520.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dly_27520/07_2023/8dly_27520.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.032 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: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 1582 2.51 5 N 417 2.21 5 O 471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 2483 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1546 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.69, per 1000 atoms: 0.68 Number of scatterers: 2483 At special positions: 0 Unit cell: (68, 82, 69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 13 16.00 O 471 8.00 N 417 7.00 C 1582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 304.6 milliseconds 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 572 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 5 sheets defined 13.4% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.619A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.081A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.330A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.505A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.660A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.815A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.124A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 186 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: 0.63 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 783 1.34 - 1.46: 649 1.46 - 1.58: 1102 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 2550 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" CB ASN H 50 " pdb=" CG ASN H 50 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.38e+00 bond pdb=" C ALA C 520 " pdb=" N PRO C 521 " ideal model delta sigma weight residual 1.330 1.348 -0.018 1.19e-02 7.06e+03 2.32e+00 bond pdb=" CB GLU C 465 " pdb=" CG GLU C 465 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" CG GLU C 465 " pdb=" CD GLU C 465 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.71e+00 ... (remaining 2545 not shown) Histogram of bond angle deviations from ideal: 100.44 - 107.16: 85 107.16 - 113.88: 1306 113.88 - 120.59: 1034 120.59 - 127.31: 1011 127.31 - 134.02: 33 Bond angle restraints: 3469 Sorted by residual: angle pdb=" CB GLU C 465 " pdb=" CG GLU C 465 " pdb=" CD GLU C 465 " ideal model delta sigma weight residual 112.60 118.87 -6.27 1.70e+00 3.46e-01 1.36e+01 angle pdb=" C GLY C 476 " pdb=" N SER C 477 " pdb=" CA SER C 477 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.78e+00 angle pdb=" C VAL C 483 " pdb=" N GLU C 484 " pdb=" CA GLU C 484 " ideal model delta sigma weight residual 120.38 124.48 -4.10 1.37e+00 5.33e-01 8.95e+00 angle pdb=" N LEU C 518 " pdb=" CA LEU C 518 " pdb=" C LEU C 518 " ideal model delta sigma weight residual 110.80 117.14 -6.34 2.13e+00 2.20e-01 8.87e+00 angle pdb=" CA LEU H 63 " pdb=" CB LEU H 63 " pdb=" CG LEU H 63 " ideal model delta sigma weight residual 116.30 125.90 -9.60 3.50e+00 8.16e-02 7.52e+00 ... (remaining 3464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.75: 1289 13.75 - 27.50: 144 27.50 - 41.25: 36 41.25 - 54.99: 9 54.99 - 68.74: 1 Dihedral angle restraints: 1479 sinusoidal: 572 harmonic: 907 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 126.09 -33.09 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CA ASN C 487 " pdb=" C ASN C 487 " pdb=" N CYS C 488 " pdb=" CA CYS C 488 " ideal model delta harmonic sigma weight residual 180.00 -164.29 -15.71 0 5.00e+00 4.00e-02 9.87e+00 dihedral pdb=" CG ARG C 509 " pdb=" CD ARG C 509 " pdb=" NE ARG C 509 " pdb=" CZ ARG C 509 " ideal model delta sinusoidal sigma weight residual -90.00 -131.99 41.99 2 1.50e+01 4.44e-03 9.55e+00 ... (remaining 1476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 224 0.046 - 0.093: 100 0.093 - 0.139: 38 0.139 - 0.185: 5 0.185 - 0.231: 3 Chirality restraints: 370 Sorted by residual: chirality pdb=" CB THR C 470 " pdb=" CA THR C 470 " pdb=" OG1 THR C 470 " pdb=" CG2 THR C 470 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA MET H 106 " pdb=" N MET H 106 " pdb=" C MET H 106 " pdb=" CB MET H 106 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 367 not shown) Planarity restraints: 449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 520 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C ALA C 520 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA C 520 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO C 521 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN H 60 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO H 61 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO H 61 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 61 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 40 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO H 41 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " 0.025 5.00e-02 4.00e+02 ... (remaining 446 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 789 2.83 - 3.35: 1927 3.35 - 3.87: 4036 3.87 - 4.38: 4493 4.38 - 4.90: 8057 Nonbonded interactions: 19302 Sorted by model distance: nonbonded pdb=" OD1 ASN C 450 " pdb=" OG SER H 56 " model vdw 2.317 2.440 nonbonded pdb=" NE ARG C 457 " pdb=" OD2 ASP C 467 " model vdw 2.432 2.520 nonbonded pdb=" O ILE C 418 " pdb=" N TYR C 423 " model vdw 2.487 2.520 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.505 2.440 nonbonded pdb=" O4 NAG C1301 " pdb=" O6 NAG C1301 " model vdw 2.524 2.440 ... (remaining 19297 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: 0.010 Normalize map: mean=0, sd=1: 2.600 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: 0.000 Extract box with map and model: 12.860 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.980 Find NCS groups from input model: 0.060 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:10.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 0.005 0.051 2550 Z= 0.329 Angle : 0.939 9.601 3469 Z= 0.512 Chirality : 0.059 0.231 370 Planarity : 0.006 0.053 448 Dihedral : 12.370 68.742 892 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.40), residues: 310 helix: -3.94 (0.60), residues: 26 sheet: -0.08 (0.45), residues: 104 loop : -1.03 (0.37), residues: 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.278 Fit side-chains outliers start: 1 outliers final: 2 residues processed: 100 average time/residue: 1.0902 time to fit residues: 111.4779 Evaluate side-chains 61 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.283 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.1677 time to fit residues: 0.5733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.0030 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 0.3768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 2550 Z= 0.166 Angle : 0.599 6.883 3469 Z= 0.297 Chirality : 0.044 0.132 370 Planarity : 0.005 0.032 448 Dihedral : 5.229 41.572 352 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 4.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.42), residues: 310 helix: -3.16 (0.82), residues: 26 sheet: 0.14 (0.47), residues: 98 loop : -0.58 (0.39), residues: 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.285 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 82 average time/residue: 1.1282 time to fit residues: 94.6170 Evaluate side-chains 69 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.313 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 4 average time/residue: 0.1034 time to fit residues: 0.8753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.0050 chunk 18 optimal weight: 0.0050 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.7610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 2550 Z= 0.231 Angle : 0.608 8.230 3469 Z= 0.302 Chirality : 0.044 0.139 370 Planarity : 0.004 0.032 448 Dihedral : 5.265 45.178 352 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 4.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.43), residues: 310 helix: -2.79 (0.96), residues: 26 sheet: 0.12 (0.49), residues: 98 loop : -0.54 (0.40), residues: 186 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.270 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 70 average time/residue: 1.2030 time to fit residues: 86.0846 Evaluate side-chains 68 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.263 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.0664 time to fit residues: 0.6087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.0040 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 2550 Z= 0.184 Angle : 0.584 7.537 3469 Z= 0.290 Chirality : 0.043 0.130 370 Planarity : 0.004 0.033 448 Dihedral : 5.033 43.086 352 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.44), residues: 310 helix: -2.74 (1.03), residues: 26 sheet: 0.14 (0.49), residues: 98 loop : -0.59 (0.40), residues: 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.290 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 69 average time/residue: 1.1835 time to fit residues: 83.5410 Evaluate side-chains 69 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.303 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.4276 time to fit residues: 2.1766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 2550 Z= 0.188 Angle : 0.565 7.513 3469 Z= 0.286 Chirality : 0.043 0.129 370 Planarity : 0.004 0.027 448 Dihedral : 4.918 42.367 352 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 4.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.44), residues: 310 helix: -2.63 (1.07), residues: 26 sheet: -0.11 (0.47), residues: 105 loop : -0.67 (0.42), residues: 179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.293 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 71 average time/residue: 1.2391 time to fit residues: 90.0738 Evaluate side-chains 65 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.294 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.4840 time to fit residues: 2.4344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.0570 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 2550 Z= 0.178 Angle : 0.604 7.281 3469 Z= 0.304 Chirality : 0.043 0.126 370 Planarity : 0.004 0.044 448 Dihedral : 4.921 40.396 352 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 4.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.44), residues: 310 helix: -2.64 (1.04), residues: 26 sheet: 0.18 (0.51), residues: 97 loop : -0.68 (0.40), residues: 187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.289 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 72 average time/residue: 1.1416 time to fit residues: 84.1320 Evaluate side-chains 68 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.3884 time to fit residues: 2.4280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.0770 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 2550 Z= 0.222 Angle : 0.616 7.210 3469 Z= 0.311 Chirality : 0.044 0.127 370 Planarity : 0.004 0.031 448 Dihedral : 5.011 42.332 352 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 3.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.44), residues: 310 helix: -2.64 (1.03), residues: 26 sheet: 0.09 (0.50), residues: 99 loop : -0.56 (0.41), residues: 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.281 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 1.3229 time to fit residues: 86.4195 Evaluate side-chains 62 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.278 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.0898 time to fit residues: 0.7135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 17 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: C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 2550 Z= 0.244 Angle : 0.664 7.923 3469 Z= 0.332 Chirality : 0.045 0.130 370 Planarity : 0.004 0.029 448 Dihedral : 5.181 44.846 352 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 4.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.45), residues: 310 helix: -2.47 (1.07), residues: 26 sheet: 0.06 (0.51), residues: 99 loop : -0.63 (0.41), residues: 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.312 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 68 average time/residue: 1.2063 time to fit residues: 83.8762 Evaluate side-chains 64 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.284 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.1066 time to fit residues: 0.8793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 2550 Z= 0.214 Angle : 0.652 8.166 3469 Z= 0.327 Chirality : 0.044 0.128 370 Planarity : 0.003 0.028 448 Dihedral : 5.004 43.630 352 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.45), residues: 310 helix: -2.49 (1.05), residues: 26 sheet: 0.19 (0.52), residues: 97 loop : -0.66 (0.41), residues: 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.259 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 69 average time/residue: 1.2293 time to fit residues: 86.6178 Evaluate side-chains 62 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.213 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1493 time to fit residues: 0.6768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.598 > 50: distance: 27 - 176: 23.670 distance: 30 - 173: 21.577 distance: 74 - 95: 21.722 distance: 90 - 95: 21.133 distance: 96 - 97: 8.657 distance: 96 - 99: 6.445 distance: 97 - 98: 14.029 distance: 97 - 103: 14.805 distance: 99 - 100: 14.180 distance: 100 - 101: 8.792 distance: 100 - 102: 12.838 distance: 103 - 104: 15.568 distance: 104 - 105: 10.442 distance: 104 - 107: 18.704 distance: 105 - 106: 16.763 distance: 105 - 115: 12.075 distance: 108 - 109: 8.903 distance: 108 - 110: 6.939 distance: 109 - 111: 28.693 distance: 110 - 112: 15.731 distance: 111 - 113: 17.548 distance: 112 - 113: 10.797 distance: 113 - 114: 7.766 distance: 115 - 116: 12.389 distance: 116 - 117: 24.018 distance: 116 - 119: 7.207 distance: 117 - 118: 11.801 distance: 117 - 124: 41.406 distance: 119 - 120: 7.035 distance: 120 - 121: 12.219 distance: 121 - 122: 14.735 distance: 122 - 123: 8.798 distance: 124 - 125: 28.279 distance: 125 - 126: 14.763 distance: 125 - 128: 12.817 distance: 126 - 127: 24.300 distance: 126 - 132: 41.164 distance: 128 - 129: 38.184 distance: 129 - 130: 13.715 distance: 129 - 131: 19.558 distance: 132 - 133: 11.696 distance: 132 - 138: 48.308 distance: 133 - 134: 14.672 distance: 133 - 136: 33.372 distance: 134 - 135: 45.774 distance: 134 - 139: 15.410 distance: 136 - 137: 35.084 distance: 137 - 138: 20.056 distance: 139 - 140: 37.150 distance: 140 - 141: 29.251 distance: 140 - 143: 42.642 distance: 141 - 142: 24.640 distance: 141 - 147: 47.082 distance: 143 - 144: 13.467 distance: 144 - 145: 28.106 distance: 144 - 146: 8.404 distance: 147 - 148: 19.420 distance: 148 - 149: 27.811 distance: 148 - 151: 16.061 distance: 149 - 150: 20.678 distance: 149 - 155: 17.186 distance: 151 - 152: 20.883 distance: 152 - 154: 14.319 distance: 155 - 156: 15.124 distance: 156 - 157: 29.864 distance: 156 - 159: 24.010 distance: 157 - 158: 19.938 distance: 157 - 166: 27.303 distance: 159 - 160: 21.779 distance: 160 - 161: 19.417 distance: 160 - 162: 23.492 distance: 161 - 163: 14.688 distance: 162 - 164: 19.932 distance: 163 - 165: 7.347 distance: 164 - 165: 7.202 distance: 166 - 167: 12.559 distance: 167 - 168: 38.854 distance: 167 - 170: 8.900 distance: 168 - 169: 18.105 distance: 168 - 173: 24.383 distance: 170 - 171: 31.046 distance: 170 - 172: 8.209 distance: 173 - 174: 37.697 distance: 175 - 176: 44.539 distance: 175 - 177: 23.967