Starting phenix.real_space_refine on Thu Dec 7 17:12:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvm_34132/12_2023/7yvm_34132.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvm_34132/12_2023/7yvm_34132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvm_34132/12_2023/7yvm_34132.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvm_34132/12_2023/7yvm_34132.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvm_34132/12_2023/7yvm_34132.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvm_34132/12_2023/7yvm_34132.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 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 16 5.16 5 C 1991 2.51 5 N 528 2.21 5 O 591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C ARG 97": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3126 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 821 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 870 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1435 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 80 Time building chain proxies: 2.26, per 1000 atoms: 0.72 Number of scatterers: 3126 At special positions: 0 Unit cell: (62.32, 72.16, 100.04, 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 16 16.00 O 591 8.00 N 528 7.00 C 1991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.06 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.09 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 616.7 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 9.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.134A pdb=" N SER A 83 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 86 through 90 removed outlier: 4.139A pdb=" N THR C 90 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.838A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 3.821A pdb=" N GLU A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.680A pdb=" N LEU A 11 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 85 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU A 33 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TYR A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.998A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.998A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR C 107 " --> pdb=" O ARG C 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.667A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 106 hydrogen bonds defined for protein. 252 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: 0.84 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 505 1.31 - 1.44: 942 1.44 - 1.58: 1737 1.58 - 1.71: 0 1.71 - 1.85: 20 Bond restraints: 3204 Sorted by residual: bond pdb=" C TYR C 33 " pdb=" O TYR C 33 " ideal model delta sigma weight residual 1.235 1.172 0.063 1.26e-02 6.30e+03 2.50e+01 bond pdb=" C PRO A 95 " pdb=" O PRO A 95 " ideal model delta sigma weight residual 1.240 1.186 0.055 1.12e-02 7.97e+03 2.39e+01 bond pdb=" N GLY A 101 " pdb=" CA GLY A 101 " ideal model delta sigma weight residual 1.442 1.479 -0.037 7.70e-03 1.69e+04 2.30e+01 bond pdb=" CA ASN A 93 " pdb=" C ASN A 93 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.28e-02 6.10e+03 2.16e+01 bond pdb=" C THR A 99 " pdb=" O THR A 99 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.13e-02 7.83e+03 1.90e+01 ... (remaining 3199 not shown) Histogram of bond angle deviations from ideal: 92.13 - 101.33: 8 101.33 - 110.52: 879 110.52 - 119.72: 1837 119.72 - 128.91: 1625 128.91 - 138.11: 20 Bond angle restraints: 4369 Sorted by residual: angle pdb=" C PRO A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta sigma weight residual 119.84 138.11 -18.27 1.25e+00 6.40e-01 2.14e+02 angle pdb=" N PRO B 521 " pdb=" CA PRO B 521 " pdb=" C PRO B 521 " ideal model delta sigma weight residual 112.33 92.13 20.20 1.87e+00 2.86e-01 1.17e+02 angle pdb=" C TYR A 98 " pdb=" CA TYR A 98 " pdb=" CB TYR A 98 " ideal model delta sigma weight residual 109.99 93.12 16.87 1.61e+00 3.86e-01 1.10e+02 angle pdb=" C ARG C 97 " pdb=" CA ARG C 97 " pdb=" CB ARG C 97 " ideal model delta sigma weight residual 111.23 99.22 12.01 1.68e+00 3.54e-01 5.11e+01 angle pdb=" C ARG B 454 " pdb=" CA ARG B 454 " pdb=" CB ARG B 454 " ideal model delta sigma weight residual 110.19 99.37 10.82 1.62e+00 3.81e-01 4.46e+01 ... (remaining 4364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.11: 1776 24.11 - 48.22: 86 48.22 - 72.32: 10 72.32 - 96.43: 0 96.43 - 120.54: 1 Dihedral angle restraints: 1873 sinusoidal: 667 harmonic: 1206 Sorted by residual: dihedral pdb=" CA PRO A 95 " pdb=" C PRO A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual -180.00 -59.46 -120.54 0 5.00e+00 4.00e-02 5.81e+02 dihedral pdb=" C TRP A 94 " pdb=" N TRP A 94 " pdb=" CA TRP A 94 " pdb=" CB TRP A 94 " ideal model delta harmonic sigma weight residual -122.60 -151.47 28.87 0 2.50e+00 1.60e-01 1.33e+02 dihedral pdb=" N TRP A 94 " pdb=" C TRP A 94 " pdb=" CA TRP A 94 " pdb=" CB TRP A 94 " ideal model delta harmonic sigma weight residual 122.80 151.58 -28.78 0 2.50e+00 1.60e-01 1.33e+02 ... (remaining 1870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.252: 476 0.252 - 0.504: 5 0.504 - 0.757: 0 0.757 - 1.009: 0 1.009 - 1.261: 1 Chirality restraints: 482 Sorted by residual: chirality pdb=" CA TRP A 94 " pdb=" N TRP A 94 " pdb=" C TRP A 94 " pdb=" CB TRP A 94 " both_signs ideal model delta sigma weight residual False 2.51 1.25 1.26 2.00e-01 2.50e+01 3.97e+01 chirality pdb=" CA CYS C 95 " pdb=" N CYS C 95 " pdb=" C CYS C 95 " pdb=" CB CYS C 95 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" CA TYR A 98 " pdb=" N TYR A 98 " pdb=" C TYR A 98 " pdb=" CB TYR A 98 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 479 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 90 " -0.036 2.00e-02 2.50e+03 7.38e-02 5.45e+01 pdb=" C GLN A 90 " 0.128 2.00e-02 2.50e+03 pdb=" O GLN A 90 " -0.047 2.00e-02 2.50e+03 pdb=" N TYR A 91 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 94 " -0.086 5.00e-02 4.00e+02 1.34e-01 2.87e+01 pdb=" N PRO A 95 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 94 " 0.049 2.00e-02 2.50e+03 2.66e-02 1.77e+01 pdb=" CG TRP A 94 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 94 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 94 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 94 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 94 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 94 " -0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 94 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 94 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A 94 " 0.017 2.00e-02 2.50e+03 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 205 2.71 - 3.26: 3153 3.26 - 3.81: 4790 3.81 - 4.35: 5932 4.35 - 4.90: 9876 Nonbonded interactions: 23956 Sorted by model distance: nonbonded pdb=" OH TYR A 98 " pdb=" OG1 THR C 105 " model vdw 2.166 2.440 nonbonded pdb=" O SER A 77 " pdb=" NE2 GLN A 79 " model vdw 2.275 2.520 nonbonded pdb=" NH1 ARG C 66 " pdb=" O ASN C 83 " model vdw 2.349 2.520 nonbonded pdb=" O LEU B 518 " pdb=" C HIS B 519 " model vdw 2.357 3.270 nonbonded pdb=" SD MET A 4 " pdb=" OE1 GLN A 90 " model vdw 2.363 3.400 ... (remaining 23951 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.370 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: 27.320 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.910 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.009 0.063 3204 Z= 0.602 Angle : 1.377 20.197 4369 Z= 0.858 Chirality : 0.092 1.261 482 Planarity : 0.009 0.134 566 Dihedral : 13.483 120.539 1091 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 28.59 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.94 % Favored : 90.58 % Rotamer: Outliers : 1.57 % Allowed : 7.55 % Favored : 90.88 % Cbeta Deviations : 1.57 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -4.19 (0.34), residues: 414 helix: -4.90 (0.26), residues: 21 sheet: -1.69 (0.41), residues: 127 loop : -3.36 (0.31), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.008 TRP C 47 HIS 0.001 0.000 HIS B 505 PHE 0.034 0.003 PHE B 347 TYR 0.044 0.003 TYR B 380 ARG 0.010 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 106 average time/residue: 0.1703 time to fit residues: 21.3385 Evaluate side-chains 60 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1689 time to fit residues: 1.2236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN B 422 ASN B 493 GLN B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 3204 Z= 0.253 Angle : 0.742 9.249 4369 Z= 0.382 Chirality : 0.047 0.253 482 Planarity : 0.006 0.087 566 Dihedral : 5.526 53.926 458 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.59 % Favored : 94.93 % Rotamer: Outliers : 3.46 % Allowed : 16.67 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -2.86 (0.38), residues: 414 helix: -3.64 (0.70), residues: 23 sheet: -1.21 (0.42), residues: 133 loop : -2.20 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 47 HIS 0.001 0.000 HIS B 519 PHE 0.016 0.002 PHE B 400 TYR 0.019 0.002 TYR A 49 ARG 0.003 0.000 ARG C 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 73 average time/residue: 0.1830 time to fit residues: 15.6807 Evaluate side-chains 64 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0290 time to fit residues: 0.6157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 10 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 3204 Z= 0.243 Angle : 0.682 9.630 4369 Z= 0.352 Chirality : 0.046 0.295 482 Planarity : 0.005 0.068 566 Dihedral : 5.152 50.875 458 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.56 % Favored : 94.20 % Rotamer: Outliers : 2.52 % Allowed : 21.07 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -2.16 (0.40), residues: 414 helix: -2.72 (0.81), residues: 29 sheet: -0.87 (0.42), residues: 135 loop : -1.63 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 47 HIS 0.000 0.000 HIS B 519 PHE 0.031 0.002 PHE B 392 TYR 0.017 0.001 TYR A 49 ARG 0.002 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 70 average time/residue: 0.1689 time to fit residues: 14.1437 Evaluate side-chains 63 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0299 time to fit residues: 0.6783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.0010 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3204 Z= 0.204 Angle : 0.651 8.201 4369 Z= 0.335 Chirality : 0.044 0.208 482 Planarity : 0.005 0.075 566 Dihedral : 5.009 44.981 458 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.09 % Allowed : 21.07 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.64 (0.41), residues: 414 helix: -2.17 (1.00), residues: 21 sheet: -0.32 (0.45), residues: 130 loop : -1.45 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 47 HIS 0.001 0.000 HIS B 505 PHE 0.028 0.002 PHE B 377 TYR 0.015 0.001 TYR A 49 ARG 0.002 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 69 average time/residue: 0.1873 time to fit residues: 15.2450 Evaluate side-chains 59 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.346 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0456 time to fit residues: 0.6966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 3204 Z= 0.339 Angle : 0.761 15.202 4369 Z= 0.392 Chirality : 0.046 0.248 482 Planarity : 0.006 0.075 566 Dihedral : 5.440 49.759 458 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.14 % Allowed : 21.07 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.79 (0.40), residues: 414 helix: -2.20 (0.82), residues: 27 sheet: -0.21 (0.44), residues: 133 loop : -1.68 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 353 HIS 0.001 0.000 HIS B 505 PHE 0.023 0.002 PHE B 392 TYR 0.024 0.002 TYR A 98 ARG 0.005 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 0.1835 time to fit residues: 14.5446 Evaluate side-chains 61 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0333 time to fit residues: 0.8936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 chunk 32 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN B 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 3204 Z= 0.212 Angle : 0.676 14.039 4369 Z= 0.345 Chirality : 0.044 0.212 482 Planarity : 0.005 0.065 566 Dihedral : 5.032 46.135 458 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.20 % Allowed : 21.07 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.53 (0.41), residues: 414 helix: -1.81 (1.04), residues: 21 sheet: -0.15 (0.45), residues: 139 loop : -1.49 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 353 HIS 0.001 0.000 HIS B 505 PHE 0.019 0.002 PHE B 392 TYR 0.013 0.001 TYR A 98 ARG 0.004 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 65 average time/residue: 0.1705 time to fit residues: 13.3323 Evaluate side-chains 62 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0416 time to fit residues: 0.6959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 3204 Z= 0.231 Angle : 0.683 13.731 4369 Z= 0.350 Chirality : 0.044 0.208 482 Planarity : 0.005 0.064 566 Dihedral : 4.996 42.928 458 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.94 % Allowed : 25.16 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.58 (0.41), residues: 414 helix: -1.73 (0.92), residues: 27 sheet: 0.00 (0.44), residues: 143 loop : -1.68 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 353 HIS 0.001 0.000 HIS B 505 PHE 0.014 0.002 PHE C 67 TYR 0.012 0.001 TYR A 49 ARG 0.005 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.365 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.1796 time to fit residues: 12.6520 Evaluate side-chains 55 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.325 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0323 time to fit residues: 0.5465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 64.6855 > 50: distance: 20 - 145: 27.915 distance: 21 - 139: 23.751 distance: 24 - 136: 29.580 distance: 68 - 72: 29.066 distance: 72 - 73: 37.996 distance: 73 - 74: 32.591 distance: 73 - 76: 22.504 distance: 74 - 75: 21.038 distance: 74 - 84: 26.070 distance: 76 - 77: 19.392 distance: 77 - 78: 24.597 distance: 77 - 79: 18.348 distance: 78 - 80: 12.001 distance: 79 - 81: 12.730 distance: 80 - 82: 7.964 distance: 81 - 82: 7.523 distance: 82 - 83: 6.308 distance: 84 - 85: 18.610 distance: 85 - 86: 23.148 distance: 85 - 88: 20.005 distance: 86 - 87: 62.334 distance: 86 - 93: 20.105 distance: 88 - 89: 43.269 distance: 89 - 90: 36.119 distance: 90 - 91: 31.565 distance: 91 - 92: 21.974 distance: 93 - 94: 36.872 distance: 94 - 95: 33.653 distance: 94 - 97: 39.218 distance: 95 - 96: 38.788 distance: 95 - 101: 35.146 distance: 97 - 98: 28.198 distance: 98 - 99: 29.159 distance: 98 - 100: 17.767 distance: 101 - 102: 5.449 distance: 101 - 107: 21.550 distance: 102 - 103: 8.627 distance: 102 - 105: 9.483 distance: 103 - 104: 14.428 distance: 103 - 108: 32.202 distance: 105 - 106: 15.139 distance: 106 - 107: 21.435 distance: 108 - 109: 28.112 distance: 109 - 110: 23.442 distance: 109 - 112: 24.206 distance: 110 - 111: 20.593 distance: 110 - 113: 21.747 distance: 113 - 114: 26.071 distance: 114 - 115: 20.711 distance: 114 - 117: 30.859 distance: 115 - 116: 14.247 distance: 115 - 118: 27.220 distance: 118 - 119: 20.262 distance: 119 - 120: 30.845 distance: 119 - 122: 3.242 distance: 120 - 121: 27.788 distance: 120 - 129: 13.987 distance: 122 - 123: 13.178 distance: 123 - 124: 9.855 distance: 123 - 125: 12.767 distance: 124 - 126: 9.544 distance: 125 - 127: 16.647 distance: 126 - 128: 7.783 distance: 127 - 128: 10.113 distance: 129 - 130: 36.944 distance: 130 - 131: 30.056 distance: 130 - 133: 16.081 distance: 131 - 132: 7.114 distance: 131 - 136: 4.063 distance: 133 - 134: 13.731 distance: 133 - 135: 13.045 distance: 136 - 137: 24.321 distance: 137 - 138: 26.095 distance: 138 - 139: 16.150 distance: 138 - 140: 19.081 distance: 140 - 141: 17.035 distance: 141 - 142: 26.951 distance: 141 - 144: 14.603 distance: 142 - 143: 41.286 distance: 142 - 146: 29.324 distance: 143 - 188: 31.153 distance: 144 - 145: 17.825