Starting phenix.real_space_refine on Mon Sep 23 12:22:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sek_40419/09_2024/8sek_40419_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sek_40419/09_2024/8sek_40419.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/8sek_40419/09_2024/8sek_40419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sek_40419/09_2024/8sek_40419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sek_40419/09_2024/8sek_40419_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sek_40419/09_2024/8sek_40419_neut.cif" } 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= -0.005 sd= 0.978 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 10 5.16 5 C 1540 2.51 5 N 400 2.21 5 O 430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2380 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 238 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.56, per 1000 atoms: 0.66 Number of scatterers: 2380 At special positions: 0 Unit cell: (75.888, 60.078, 41.106, 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 10 16.00 O 430 8.00 N 400 7.00 C 1540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 297.2 milliseconds 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.558A pdb=" N TYR A 10 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR C 10 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR E 10 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR G 10 " --> pdb=" O GLU I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.890A pdb=" N ILE C 31 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 32 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY C 33 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE E 31 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 32 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY E 33 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE G 31 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE E 32 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY G 33 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE I 31 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE G 32 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY I 33 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.558A pdb=" N TYR B 10 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR D 10 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR F 10 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR H 10 " --> pdb=" O GLU J 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 17 Processing sheet with id=AA7, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AA8, first strand: chain 'B' and resid 30 through 36 removed outlier: 6.889A pdb=" N ILE D 31 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 32 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY D 33 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE F 31 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE D 32 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY F 33 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE H 31 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE F 32 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY H 33 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE J 31 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE H 32 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY J 33 " --> pdb=" O ILE H 32 " (cutoff:3.500A) 48 hydrogen bonds defined for protein. 144 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: 0.59 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 675 1.32 - 1.44: 515 1.44 - 1.56: 1210 1.56 - 1.68: 0 1.68 - 1.79: 20 Bond restraints: 2420 Sorted by residual: bond pdb=" CB HIS G 13 " pdb=" CG HIS G 13 " ideal model delta sigma weight residual 1.497 1.376 0.121 1.40e-02 5.10e+03 7.50e+01 bond pdb=" CB HIS E 13 " pdb=" CG HIS E 13 " ideal model delta sigma weight residual 1.497 1.376 0.121 1.40e-02 5.10e+03 7.50e+01 bond pdb=" CB HIS D 13 " pdb=" CG HIS D 13 " ideal model delta sigma weight residual 1.497 1.376 0.121 1.40e-02 5.10e+03 7.50e+01 bond pdb=" CB HIS C 13 " pdb=" CG HIS C 13 " ideal model delta sigma weight residual 1.497 1.376 0.121 1.40e-02 5.10e+03 7.48e+01 bond pdb=" CB HIS B 13 " pdb=" CG HIS B 13 " ideal model delta sigma weight residual 1.497 1.376 0.121 1.40e-02 5.10e+03 7.48e+01 ... (remaining 2415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 2374 1.97 - 3.95: 578 3.95 - 5.92: 148 5.92 - 7.89: 100 7.89 - 9.87: 50 Bond angle restraints: 3250 Sorted by residual: angle pdb=" N HIS H 13 " pdb=" CA HIS H 13 " pdb=" C HIS H 13 " ideal model delta sigma weight residual 108.75 116.85 -8.10 9.60e-01 1.09e+00 7.12e+01 angle pdb=" N HIS G 13 " pdb=" CA HIS G 13 " pdb=" C HIS G 13 " ideal model delta sigma weight residual 108.75 116.85 -8.10 9.60e-01 1.09e+00 7.12e+01 angle pdb=" N HIS J 13 " pdb=" CA HIS J 13 " pdb=" C HIS J 13 " ideal model delta sigma weight residual 108.75 116.85 -8.10 9.60e-01 1.09e+00 7.11e+01 angle pdb=" N HIS D 13 " pdb=" CA HIS D 13 " pdb=" C HIS D 13 " ideal model delta sigma weight residual 108.75 116.83 -8.08 9.60e-01 1.09e+00 7.09e+01 angle pdb=" N HIS I 13 " pdb=" CA HIS I 13 " pdb=" C HIS I 13 " ideal model delta sigma weight residual 108.75 116.82 -8.07 9.60e-01 1.09e+00 7.07e+01 ... (remaining 3245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.02: 1190 10.02 - 20.03: 90 20.03 - 30.04: 40 30.04 - 40.06: 10 40.06 - 50.07: 10 Dihedral angle restraints: 1340 sinusoidal: 500 harmonic: 840 Sorted by residual: dihedral pdb=" C PHE G 20 " pdb=" N PHE G 20 " pdb=" CA PHE G 20 " pdb=" CB PHE G 20 " ideal model delta harmonic sigma weight residual -122.60 -116.11 -6.49 0 2.50e+00 1.60e-01 6.74e+00 dihedral pdb=" C PHE E 20 " pdb=" N PHE E 20 " pdb=" CA PHE E 20 " pdb=" CB PHE E 20 " ideal model delta harmonic sigma weight residual -122.60 -116.13 -6.47 0 2.50e+00 1.60e-01 6.70e+00 dihedral pdb=" C PHE I 20 " pdb=" N PHE I 20 " pdb=" CA PHE I 20 " pdb=" CB PHE I 20 " ideal model delta harmonic sigma weight residual -122.60 -116.13 -6.47 0 2.50e+00 1.60e-01 6.69e+00 ... (remaining 1337 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.074: 159 0.074 - 0.143: 121 0.143 - 0.211: 20 0.211 - 0.280: 30 0.280 - 0.348: 30 Chirality restraints: 360 Sorted by residual: chirality pdb=" CA PHE J 19 " pdb=" N PHE J 19 " pdb=" C PHE J 19 " pdb=" CB PHE J 19 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA PHE B 19 " pdb=" N PHE B 19 " pdb=" C PHE B 19 " pdb=" CB PHE B 19 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA PHE E 19 " pdb=" N PHE E 19 " pdb=" C PHE E 19 " pdb=" CB PHE E 19 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 357 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 40 " -0.034 2.00e-02 2.50e+03 6.87e-02 4.72e+01 pdb=" C VAL A 40 " 0.119 2.00e-02 2.50e+03 pdb=" O VAL A 40 " -0.043 2.00e-02 2.50e+03 pdb=" OXT VAL A 40 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 40 " -0.034 2.00e-02 2.50e+03 6.87e-02 4.72e+01 pdb=" C VAL C 40 " 0.119 2.00e-02 2.50e+03 pdb=" O VAL C 40 " -0.043 2.00e-02 2.50e+03 pdb=" OXT VAL C 40 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 40 " -0.034 2.00e-02 2.50e+03 6.87e-02 4.71e+01 pdb=" C VAL G 40 " 0.119 2.00e-02 2.50e+03 pdb=" O VAL G 40 " -0.043 2.00e-02 2.50e+03 pdb=" OXT VAL G 40 " -0.042 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1058 2.90 - 3.40: 2137 3.40 - 3.90: 4274 3.90 - 4.40: 4695 4.40 - 4.90: 8761 Nonbonded interactions: 20925 Sorted by model distance: nonbonded pdb=" N LYS C 28 " pdb=" N GLY C 29 " model vdw 2.397 2.560 nonbonded pdb=" N LYS I 28 " pdb=" N GLY I 29 " model vdw 2.397 2.560 nonbonded pdb=" N LYS E 28 " pdb=" N GLY E 29 " model vdw 2.397 2.560 nonbonded pdb=" N LYS F 28 " pdb=" N GLY F 29 " model vdw 2.397 2.560 nonbonded pdb=" N LYS B 28 " pdb=" N GLY B 29 " model vdw 2.397 2.560 ... (remaining 20920 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.860 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 0.032 0.169 2420 Z= 2.143 Angle : 2.389 9.868 3250 Z= 1.617 Chirality : 0.140 0.348 360 Planarity : 0.013 0.069 420 Dihedral : 10.425 50.073 820 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.19 (0.40), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS H 13 PHE 0.018 0.005 PHE B 20 TYR 0.025 0.012 TYR F 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: F 18 VAL cc_start: 0.8270 (m) cc_final: 0.7985 (p) REVERT: G 10 TYR cc_start: 0.6926 (p90) cc_final: 0.6718 (p90) REVERT: H 19 PHE cc_start: 0.8102 (p90) cc_final: 0.7820 (p90) REVERT: I 28 LYS cc_start: 0.7658 (ptpt) cc_final: 0.5889 (mmtt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1386 time to fit residues: 14.1102 Evaluate side-chains 67 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2420 Z= 0.383 Angle : 0.848 10.012 3250 Z= 0.478 Chirality : 0.065 0.250 360 Planarity : 0.003 0.013 420 Dihedral : 7.649 23.832 330 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.33 % Favored : 83.67 % Rotamer: Outliers : 3.75 % Allowed : 10.83 % Favored : 85.42 % 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: -4.23 (0.31), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.23), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 14 PHE 0.018 0.004 PHE D 19 TYR 0.013 0.002 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 19 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7545 (p90) REVERT: D 19 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7345 (p90) REVERT: I 28 LYS cc_start: 0.7782 (ptpt) cc_final: 0.5736 (mmtt) outliers start: 9 outliers final: 2 residues processed: 76 average time/residue: 0.0945 time to fit residues: 9.0201 Evaluate side-chains 60 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain I residue 11 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7317 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2420 Z= 0.290 Angle : 0.688 6.520 3250 Z= 0.390 Chirality : 0.060 0.235 360 Planarity : 0.003 0.016 420 Dihedral : 7.851 30.218 330 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.00 % Favored : 86.00 % Rotamer: Outliers : 4.58 % Allowed : 12.92 % Favored : 82.50 % 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: -4.13 (0.32), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.24), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 14 PHE 0.018 0.003 PHE E 19 TYR 0.009 0.001 TYR I 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6956 (p90) REVERT: B 19 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.7117 (p90) REVERT: C 19 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7417 (p90) REVERT: E 19 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7819 (p90) REVERT: I 28 LYS cc_start: 0.7782 (ptpt) cc_final: 0.5726 (mmtt) REVERT: J 34 LEU cc_start: 0.7729 (tt) cc_final: 0.7412 (tt) outliers start: 11 outliers final: 3 residues processed: 66 average time/residue: 0.0955 time to fit residues: 7.9677 Evaluate side-chains 65 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain I residue 11 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 2420 Z= 0.491 Angle : 0.743 4.965 3250 Z= 0.426 Chirality : 0.061 0.258 360 Planarity : 0.003 0.020 420 Dihedral : 8.197 33.115 330 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.67 % Favored : 81.33 % Rotamer: Outliers : 5.00 % Allowed : 15.83 % Favored : 79.17 % 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: -4.27 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS J 14 PHE 0.041 0.004 PHE F 19 TYR 0.012 0.002 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7322 (p90) REVERT: B 13 HIS cc_start: 0.7100 (t-90) cc_final: 0.5673 (p-80) REVERT: B 19 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7464 (p90) REVERT: C 19 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7743 (p90) REVERT: E 18 VAL cc_start: 0.8523 (m) cc_final: 0.8267 (t) REVERT: E 19 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7955 (p90) REVERT: G 19 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.8093 (p90) REVERT: H 19 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7918 (p90) REVERT: I 28 LYS cc_start: 0.8213 (ptpt) cc_final: 0.6246 (mmtt) outliers start: 12 outliers final: 3 residues processed: 80 average time/residue: 0.0935 time to fit residues: 9.4082 Evaluate side-chains 75 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain I residue 11 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 15 GLN ** J 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2420 Z= 0.273 Angle : 0.673 8.616 3250 Z= 0.380 Chirality : 0.061 0.249 360 Planarity : 0.003 0.020 420 Dihedral : 8.274 35.839 330 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.33 % Favored : 84.67 % Rotamer: Outliers : 5.42 % Allowed : 17.92 % Favored : 76.67 % 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: -4.34 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 14 PHE 0.033 0.003 PHE F 19 TYR 0.010 0.001 TYR I 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6881 (p90) REVERT: B 13 HIS cc_start: 0.6752 (t-90) cc_final: 0.5477 (p-80) REVERT: C 19 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.7308 (p90) REVERT: D 19 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.7168 (p90) REVERT: E 18 VAL cc_start: 0.8416 (m) cc_final: 0.8083 (t) REVERT: E 19 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7630 (p90) REVERT: F 19 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7630 (p90) REVERT: H 19 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7740 (p90) REVERT: I 28 LYS cc_start: 0.7662 (ptpt) cc_final: 0.5853 (mmtt) outliers start: 13 outliers final: 2 residues processed: 79 average time/residue: 0.1005 time to fit residues: 9.9596 Evaluate side-chains 72 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 19 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 2 optimal weight: 0.0570 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2420 Z= 0.257 Angle : 0.689 7.314 3250 Z= 0.378 Chirality : 0.061 0.259 360 Planarity : 0.002 0.018 420 Dihedral : 8.551 38.534 330 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.00 % Favored : 83.00 % Rotamer: Outliers : 5.42 % Allowed : 22.50 % Favored : 72.08 % 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: -4.35 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 14 PHE 0.032 0.003 PHE F 19 TYR 0.009 0.001 TYR I 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 HIS cc_start: 0.6584 (t-90) cc_final: 0.5284 (p-80) REVERT: D 19 PHE cc_start: 0.7161 (OUTLIER) cc_final: 0.6931 (p90) REVERT: E 19 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7587 (p90) REVERT: F 19 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7575 (p90) REVERT: H 19 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7688 (p90) REVERT: I 28 LYS cc_start: 0.7627 (ptpt) cc_final: 0.5790 (mmtt) outliers start: 13 outliers final: 4 residues processed: 73 average time/residue: 0.0950 time to fit residues: 8.7181 Evaluate side-chains 69 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 32 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-dev-5461/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-dev-5461/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: 57.3085 > 50: distance: 71 - 168: 7.285 distance: 74 - 177: 11.318 distance: 84 - 180: 16.523 distance: 125 - 131: 15.305 distance: 131 - 132: 9.052 distance: 132 - 133: 10.980 distance: 132 - 135: 11.711 distance: 133 - 134: 7.921 distance: 133 - 140: 5.462 distance: 135 - 136: 9.816 distance: 136 - 137: 16.198 distance: 137 - 138: 6.526 distance: 138 - 139: 8.180 distance: 140 - 141: 15.766 distance: 141 - 142: 27.525 distance: 142 - 143: 7.855 distance: 142 - 144: 13.498 distance: 144 - 145: 9.440 distance: 145 - 146: 10.728 distance: 145 - 148: 15.810 distance: 146 - 147: 10.949 distance: 146 - 149: 9.497 distance: 149 - 150: 9.420 distance: 150 - 151: 7.058 distance: 150 - 153: 7.797 distance: 151 - 152: 15.760 distance: 151 - 157: 5.690 distance: 153 - 154: 10.569 distance: 153 - 155: 38.540 distance: 154 - 156: 19.164 distance: 157 - 158: 9.816 distance: 158 - 159: 10.906 distance: 158 - 161: 7.359 distance: 159 - 160: 17.592 distance: 159 - 165: 9.873 distance: 161 - 162: 16.198 distance: 161 - 163: 19.514 distance: 162 - 164: 19.629 distance: 165 - 166: 12.696 distance: 166 - 167: 10.943 distance: 167 - 168: 5.988 distance: 167 - 169: 8.389 distance: 169 - 170: 8.738 distance: 169 - 254: 7.635 distance: 170 - 171: 6.798 distance: 170 - 173: 16.750 distance: 171 - 172: 4.190 distance: 171 - 177: 6.693 distance: 172 - 263: 16.045 distance: 173 - 174: 13.586 distance: 174 - 175: 15.985 distance: 174 - 176: 21.970 distance: 177 - 178: 11.270 distance: 178 - 179: 14.446 distance: 178 - 181: 3.038 distance: 179 - 180: 7.264 distance: 179 - 185: 7.027 distance: 182 - 183: 12.494 distance: 183 - 184: 13.981 distance: 185 - 186: 12.242 distance: 185 - 266: 6.655 distance: 186 - 187: 19.546 distance: 186 - 189: 16.616 distance: 187 - 188: 37.061 distance: 187 - 192: 25.932 distance: 189 - 190: 23.792 distance: 189 - 191: 21.398 distance: 193 - 194: 24.833 distance: 194 - 195: 25.148 distance: 194 - 196: 15.414