Starting phenix.real_space_refine (version: dev) on Fri Mar 17 20:59:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9m_16511/03_2023/8c9m_16511.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9m_16511/03_2023/8c9m_16511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9m_16511/03_2023/8c9m_16511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9m_16511/03_2023/8c9m_16511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9m_16511/03_2023/8c9m_16511.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9m_16511/03_2023/8c9m_16511.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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 Process input model Symmetric amino acids flipped Residue "A TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 21480 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3580 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "B" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3580 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "C" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3580 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "D" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3580 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "E" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3580 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "F" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3580 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Time building chain proxies: 9.55, per 1000 atoms: 0.44 Number of scatterers: 21480 At special positions: 0 Unit cell: (121.743, 121.743, 96.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 O 2004 8.00 N 1890 7.00 C 6762 6.00 H 10752 1.00 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 - 3.50 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: 18.70 Conformation dependent library (CDL) restraints added in 1.9 seconds 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 0 sheets defined 73.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 9 through 23 Processing helix chain 'A' and resid 26 through 40 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 56 through 80 Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 109 through 126 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 147 through 163 Processing helix chain 'A' and resid 165 through 180 Processing helix chain 'A' and resid 182 through 190 removed outlier: 4.213A pdb=" N ALA A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 210 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'B' and resid 9 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 43 through 53 Processing helix chain 'B' and resid 56 through 80 Processing helix chain 'B' and resid 88 through 94 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 109 through 126 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 147 through 163 Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 182 through 190 removed outlier: 4.213A pdb=" N ALA B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 43 through 53 Processing helix chain 'C' and resid 56 through 80 Processing helix chain 'C' and resid 88 through 94 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 109 through 126 Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 147 through 163 Processing helix chain 'C' and resid 165 through 180 Processing helix chain 'C' and resid 182 through 190 removed outlier: 4.213A pdb=" N ALA C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 210 Processing helix chain 'C' and resid 215 through 228 Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 26 through 40 Processing helix chain 'D' and resid 43 through 53 Processing helix chain 'D' and resid 56 through 80 Processing helix chain 'D' and resid 88 through 94 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 109 through 126 Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 147 through 163 Processing helix chain 'D' and resid 165 through 180 Processing helix chain 'D' and resid 182 through 190 removed outlier: 4.214A pdb=" N ALA D 188 " --> pdb=" O GLU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 210 Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'E' and resid 9 through 23 Processing helix chain 'E' and resid 26 through 40 Processing helix chain 'E' and resid 43 through 53 Processing helix chain 'E' and resid 56 through 80 Processing helix chain 'E' and resid 88 through 94 Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 109 through 126 Processing helix chain 'E' and resid 135 through 139 Processing helix chain 'E' and resid 147 through 163 Processing helix chain 'E' and resid 165 through 180 Processing helix chain 'E' and resid 182 through 190 removed outlier: 4.213A pdb=" N ALA E 188 " --> pdb=" O GLU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 210 Processing helix chain 'E' and resid 215 through 228 Processing helix chain 'F' and resid 9 through 23 Processing helix chain 'F' and resid 26 through 40 Processing helix chain 'F' and resid 43 through 53 Processing helix chain 'F' and resid 56 through 80 Processing helix chain 'F' and resid 88 through 94 Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 109 through 126 Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 147 through 163 Processing helix chain 'F' and resid 165 through 180 Processing helix chain 'F' and resid 182 through 190 removed outlier: 4.213A pdb=" N ALA F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'F' and resid 215 through 228 696 hydrogen bonds defined for protein. 2052 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: 7.98 Time building geometry restraints manager: 19.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 10728 1.11 - 1.29: 1939 1.29 - 1.46: 3905 1.46 - 1.63: 5010 1.63 - 1.81: 120 Bond restraints: 21702 Sorted by residual: bond pdb=" CA TRP F 67 " pdb=" C TRP F 67 " ideal model delta sigma weight residual 1.524 1.386 0.138 1.27e-02 6.20e+03 1.18e+02 bond pdb=" CA TRP B 67 " pdb=" C TRP B 67 " ideal model delta sigma weight residual 1.524 1.386 0.137 1.27e-02 6.20e+03 1.17e+02 bond pdb=" CA TRP D 67 " pdb=" C TRP D 67 " ideal model delta sigma weight residual 1.524 1.386 0.137 1.27e-02 6.20e+03 1.17e+02 bond pdb=" CA TRP A 67 " pdb=" C TRP A 67 " ideal model delta sigma weight residual 1.524 1.386 0.137 1.27e-02 6.20e+03 1.17e+02 bond pdb=" CA TRP C 67 " pdb=" C TRP C 67 " ideal model delta sigma weight residual 1.524 1.386 0.137 1.27e-02 6.20e+03 1.17e+02 ... (remaining 21697 not shown) Histogram of bond angle deviations from ideal: 93.14 - 101.32: 55 101.32 - 109.50: 16005 109.50 - 117.68: 12262 117.68 - 125.86: 10765 125.86 - 134.04: 255 Bond angle restraints: 39342 Sorted by residual: angle pdb=" C GLY E 23 " pdb=" N PRO E 24 " pdb=" CA PRO E 24 " ideal model delta sigma weight residual 119.32 128.46 -9.14 1.14e+00 7.69e-01 6.43e+01 angle pdb=" C GLY D 23 " pdb=" N PRO D 24 " pdb=" CA PRO D 24 " ideal model delta sigma weight residual 119.32 128.44 -9.12 1.14e+00 7.69e-01 6.40e+01 angle pdb=" C GLY C 23 " pdb=" N PRO C 24 " pdb=" CA PRO C 24 " ideal model delta sigma weight residual 119.32 128.43 -9.11 1.14e+00 7.69e-01 6.39e+01 angle pdb=" C GLY F 23 " pdb=" N PRO F 24 " pdb=" CA PRO F 24 " ideal model delta sigma weight residual 119.32 128.42 -9.10 1.14e+00 7.69e-01 6.37e+01 angle pdb=" C GLY A 23 " pdb=" N PRO A 24 " pdb=" CA PRO A 24 " ideal model delta sigma weight residual 119.32 128.42 -9.10 1.14e+00 7.69e-01 6.37e+01 ... (remaining 39337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.79: 8419 14.79 - 29.58: 167 29.58 - 44.38: 41 44.38 - 59.17: 31 59.17 - 73.96: 6 Dihedral angle restraints: 8664 sinusoidal: 4128 harmonic: 4536 Sorted by residual: dihedral pdb=" CD2 HIS C 40 " pdb=" CG HIS C 40 " pdb=" ND1 HIS C 40 " pdb=" HD1 HIS C 40 " ideal model delta harmonic sigma weight residual -180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CD2 HIS F 40 " pdb=" CG HIS F 40 " pdb=" ND1 HIS F 40 " pdb=" HD1 HIS F 40 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CD2 HIS E 40 " pdb=" CG HIS E 40 " pdb=" ND1 HIS E 40 " pdb=" HD1 HIS E 40 " ideal model delta harmonic sigma weight residual -180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 8661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 784 0.073 - 0.147: 475 0.147 - 0.220: 273 0.220 - 0.293: 46 0.293 - 0.367: 18 Chirality restraints: 1596 Sorted by residual: chirality pdb=" CA TRP C 67 " pdb=" N TRP C 67 " pdb=" C TRP C 67 " pdb=" CB TRP C 67 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA TRP D 67 " pdb=" N TRP D 67 " pdb=" C TRP D 67 " pdb=" CB TRP D 67 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA TRP A 67 " pdb=" N TRP A 67 " pdb=" C TRP A 67 " pdb=" CB TRP A 67 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 1593 not shown) Planarity restraints: 3216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 40 " -0.100 2.00e-02 2.50e+03 9.60e-02 2.08e+02 pdb=" CG HIS C 40 " -0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS C 40 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 HIS C 40 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS C 40 " -0.049 2.00e-02 2.50e+03 pdb=" NE2 HIS C 40 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 HIS C 40 " 0.221 2.00e-02 2.50e+03 pdb=" HD2 HIS C 40 " 0.075 2.00e-02 2.50e+03 pdb=" HE1 HIS C 40 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 40 " -0.100 2.00e-02 2.50e+03 9.60e-02 2.07e+02 pdb=" CG HIS F 40 " -0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS F 40 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 HIS F 40 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 HIS F 40 " -0.049 2.00e-02 2.50e+03 pdb=" NE2 HIS F 40 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 HIS F 40 " 0.221 2.00e-02 2.50e+03 pdb=" HD2 HIS F 40 " 0.075 2.00e-02 2.50e+03 pdb=" HE1 HIS F 40 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 40 " -0.100 2.00e-02 2.50e+03 9.58e-02 2.06e+02 pdb=" CG HIS E 40 " -0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS E 40 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 HIS E 40 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 HIS E 40 " -0.049 2.00e-02 2.50e+03 pdb=" NE2 HIS E 40 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 HIS E 40 " 0.220 2.00e-02 2.50e+03 pdb=" HD2 HIS E 40 " 0.075 2.00e-02 2.50e+03 pdb=" HE1 HIS E 40 " -0.079 2.00e-02 2.50e+03 ... (remaining 3213 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1403 2.18 - 2.78: 41478 2.78 - 3.39: 59201 3.39 - 3.99: 74874 3.99 - 4.60: 114212 Nonbonded interactions: 291168 Sorted by model distance: nonbonded pdb=" OG SER E 100 " pdb=" H THR E 101 " model vdw 1.575 1.850 nonbonded pdb=" OG SER F 100 " pdb=" H THR F 101 " model vdw 1.575 1.850 nonbonded pdb=" OG SER B 100 " pdb=" H THR B 101 " model vdw 1.575 1.850 nonbonded pdb=" OG SER A 100 " pdb=" H THR A 101 " model vdw 1.576 1.850 nonbonded pdb=" OG SER D 100 " pdb=" H THR D 101 " model vdw 1.576 1.850 ... (remaining 291163 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 72 5.16 5 C 6762 2.51 5 N 1890 2.21 5 O 2004 1.98 5 H 10752 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.340 Extract box with map and model: 6.070 Check model and map are aligned: 0.280 Process input model: 67.340 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 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 : 0.023 0.138 10950 Z= 1.466 Angle : 1.427 10.186 14802 Z= 1.014 Chirality : 0.115 0.367 1596 Planarity : 0.012 0.053 1932 Dihedral : 9.581 73.959 4176 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.88 % Allowed : 2.65 % Favored : 96.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1356 helix: -0.10 (0.15), residues: 942 sheet: None (None), residues: 0 loop : -0.73 (0.29), residues: 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symTraceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 318, in caller self.log.flush() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/libtbx/utils.py", line 1570, in flush if (flush is not None): flush() IOError: [Errno 28] No space left on device