Starting phenix.real_space_refine on Sat Aug 3 07:34:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bys_16332/08_2024/8bys_16332.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bys_16332/08_2024/8bys_16332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bys_16332/08_2024/8bys_16332.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bys_16332/08_2024/8bys_16332.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bys_16332/08_2024/8bys_16332.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bys_16332/08_2024/8bys_16332.cif" } resolution = 3.28 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= -0.000 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 9 5.16 5 C 4579 2.51 5 N 1325 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7406 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2470 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 2, 'TRANS': 320} Chain: "B" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2466 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 2, 'TRANS': 319} Chain: "C" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2470 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 2, 'TRANS': 320} Time building chain proxies: 5.86, per 1000 atoms: 0.79 Number of scatterers: 7406 At special positions: 0 Unit cell: (84.952, 94.136, 95.284, 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 9 16.00 O 1493 8.00 N 1325 7.00 C 4579 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 - 3.50 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: 2.82 Conformation dependent library (CDL) restraints added in 1.4 seconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 6 sheets defined 5.3% alpha, 56.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 100 through 113 Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.581A pdb=" N ARG B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 4.038A pdb=" N ALA B 243 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 114 removed outlier: 3.543A pdb=" N ASP C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 removed outlier: 4.020A pdb=" N ALA C 243 " --> pdb=" O ASP C 240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 130 removed outlier: 6.866A pdb=" N THR A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 185 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS A 167 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE A 183 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 24.083A pdb=" N THR A 182 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 18.720A pdb=" N THR A 206 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 12.803A pdb=" N ASP A 184 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLN A 204 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR A 213 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS A 376 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 400 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 283 Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 130 removed outlier: 6.575A pdb=" N THR B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 185 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS B 167 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE B 183 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ASN B 169 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ALA B 181 " --> pdb=" O ASN B 169 " (cutoff:3.500A) removed outlier: 23.957A pdb=" N THR B 182 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 18.730A pdb=" N THR B 206 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 12.867A pdb=" N ASP B 184 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLN B 204 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS B 376 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER B 400 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 279 through 283 Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 130 removed outlier: 6.752A pdb=" N THR C 160 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 185 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS C 167 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILE C 183 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASN C 169 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA C 181 " --> pdb=" O ASN C 169 " (cutoff:3.500A) removed outlier: 23.941A pdb=" N THR C 182 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 18.576A pdb=" N THR C 206 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 12.761A pdb=" N ASP C 184 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLN C 204 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS C 376 " --> pdb=" O SER C 400 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER C 400 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 279 through 283 465 hydrogen bonds defined for protein. 1311 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: 2.48 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2540 1.34 - 1.45: 1259 1.45 - 1.57: 3724 1.57 - 1.69: 0 1.69 - 1.80: 18 Bond restraints: 7541 Sorted by residual: bond pdb=" CG ASP C 218 " pdb=" OD1 ASP C 218 " ideal model delta sigma weight residual 1.249 1.230 0.019 1.90e-02 2.77e+03 1.03e+00 bond pdb=" CB ILE C 239 " pdb=" CG1 ILE C 239 " ideal model delta sigma weight residual 1.530 1.511 0.019 2.00e-02 2.50e+03 9.31e-01 bond pdb=" CA ASP C 214 " pdb=" C ASP C 214 " ideal model delta sigma weight residual 1.530 1.522 0.009 1.08e-02 8.57e+03 6.73e-01 bond pdb=" CB ASP C 218 " pdb=" CG ASP C 218 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.43e-01 bond pdb=" N GLY A 261 " pdb=" CA GLY A 261 " ideal model delta sigma weight residual 1.456 1.447 0.009 1.16e-02 7.43e+03 5.70e-01 ... (remaining 7536 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.89: 72 106.89 - 113.67: 3919 113.67 - 120.46: 2828 120.46 - 127.25: 3304 127.25 - 134.04: 42 Bond angle restraints: 10165 Sorted by residual: angle pdb=" N ASP B 215 " pdb=" CA ASP B 215 " pdb=" C ASP B 215 " ideal model delta sigma weight residual 107.73 113.36 -5.63 1.34e+00 5.57e-01 1.77e+01 angle pdb=" C ASP C 215 " pdb=" N THR C 216 " pdb=" CA THR C 216 " ideal model delta sigma weight residual 120.90 125.84 -4.94 1.41e+00 5.03e-01 1.23e+01 angle pdb=" CA PHE B 203 " pdb=" C PHE B 203 " pdb=" N GLN B 204 " ideal model delta sigma weight residual 115.54 120.09 -4.55 1.52e+00 4.33e-01 8.95e+00 angle pdb=" CA PHE B 203 " pdb=" C PHE B 203 " pdb=" O PHE B 203 " ideal model delta sigma weight residual 121.60 118.32 3.28 1.21e+00 6.83e-01 7.36e+00 angle pdb=" C ALA C 138 " pdb=" N ASN C 139 " pdb=" CA ASN C 139 " ideal model delta sigma weight residual 121.54 126.50 -4.96 1.91e+00 2.74e-01 6.75e+00 ... (remaining 10160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4015 17.98 - 35.96: 284 35.96 - 53.94: 45 53.94 - 71.92: 16 71.92 - 89.90: 7 Dihedral angle restraints: 4367 sinusoidal: 1662 harmonic: 2705 Sorted by residual: dihedral pdb=" CA ASP C 214 " pdb=" CB ASP C 214 " pdb=" CG ASP C 214 " pdb=" OD1 ASP C 214 " ideal model delta sinusoidal sigma weight residual -30.00 -87.63 57.63 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP A 367 " pdb=" C ASP A 367 " pdb=" N LEU A 368 " pdb=" CA LEU A 368 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA TYR A 213 " pdb=" C TYR A 213 " pdb=" N ASP A 214 " pdb=" CA ASP A 214 " ideal model delta harmonic sigma weight residual 180.00 163.94 16.06 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 4364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 444 0.026 - 0.052: 371 0.052 - 0.077: 139 0.077 - 0.103: 38 0.103 - 0.129: 40 Chirality restraints: 1032 Sorted by residual: chirality pdb=" CA VAL B 224 " pdb=" N VAL B 224 " pdb=" C VAL B 224 " pdb=" CB VAL B 224 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ASN B 321 " pdb=" N ASN B 321 " pdb=" C ASN B 321 " pdb=" CB ASN B 321 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA VAL C 163 " pdb=" N VAL C 163 " pdb=" C VAL C 163 " pdb=" CB VAL C 163 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1029 not shown) Planarity restraints: 1367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 214 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.41e+00 pdb=" C ASP C 214 " -0.021 2.00e-02 2.50e+03 pdb=" O ASP C 214 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP C 215 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 139 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.07e+00 pdb=" C ASN C 139 " -0.018 2.00e-02 2.50e+03 pdb=" O ASN C 139 " 0.007 2.00e-02 2.50e+03 pdb=" N SER C 140 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 420 " -0.004 2.00e-02 2.50e+03 7.28e-03 9.27e-01 pdb=" CG PHE A 420 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 420 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 420 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 420 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 420 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 420 " 0.001 2.00e-02 2.50e+03 ... (remaining 1364 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 524 2.74 - 3.28: 6826 3.28 - 3.82: 11482 3.82 - 4.36: 14516 4.36 - 4.90: 27290 Nonbonded interactions: 60638 Sorted by model distance: nonbonded pdb=" OD2 ASP B 215 " pdb=" OG SER B 359 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR C 206 " pdb=" OD2 ASP C 214 " model vdw 2.200 3.040 nonbonded pdb=" O VAL A 263 " pdb=" OG SER A 267 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR A 206 " pdb=" OD2 ASP A 214 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR B 206 " pdb=" OD1 ASP B 214 " model vdw 2.235 3.040 ... (remaining 60633 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' and resid 100 through 421) selection = chain 'B' selection = (chain 'C' and resid 100 through 421) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 23.980 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 7541 Z= 0.243 Angle : 0.563 7.741 10165 Z= 0.325 Chirality : 0.044 0.129 1032 Planarity : 0.002 0.032 1367 Dihedral : 13.509 89.900 2687 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.29), residues: 962 helix: 1.49 (0.97), residues: 41 sheet: -0.36 (0.22), residues: 588 loop : -1.11 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 325 HIS 0.004 0.002 HIS C 283 PHE 0.016 0.002 PHE A 420 TYR 0.013 0.002 TYR B 235 ARG 0.004 0.000 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.781 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1685 time to fit residues: 12.0216 Evaluate side-chains 35 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 221 GLN A 223 ASN A 246 ASN A 305 ASN A 417 ASN B 180 GLN B 232 GLN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7541 Z= 0.341 Angle : 0.590 8.391 10165 Z= 0.336 Chirality : 0.046 0.132 1032 Planarity : 0.003 0.025 1367 Dihedral : 4.638 15.856 1064 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.26 % Allowed : 6.56 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.28), residues: 962 helix: 1.51 (0.93), residues: 41 sheet: -0.30 (0.22), residues: 579 loop : -1.45 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 325 HIS 0.005 0.002 HIS B 190 PHE 0.020 0.002 PHE A 217 TYR 0.014 0.002 TYR B 235 ARG 0.003 0.000 ARG C 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.841 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 44 average time/residue: 0.1710 time to fit residues: 11.5021 Evaluate side-chains 37 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 122 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 58.1821 > 50: distance: 20 - 156: 9.682 distance: 23 - 153: 5.860 distance: 29 - 143: 3.568 distance: 32 - 140: 12.841 distance: 39 - 127: 14.375 distance: 42 - 124: 13.267 distance: 77 - 82: 9.482 distance: 82 - 83: 3.896 distance: 83 - 84: 5.938 distance: 83 - 86: 4.258 distance: 84 - 85: 7.345 distance: 84 - 91: 6.817 distance: 86 - 87: 10.929 distance: 87 - 88: 12.472 distance: 88 - 89: 12.690 distance: 89 - 90: 21.148 distance: 91 - 92: 5.647 distance: 93 - 94: 7.382 distance: 93 - 95: 6.675 distance: 95 - 96: 32.413 distance: 96 - 97: 28.448 distance: 96 - 99: 18.446 distance: 97 - 98: 12.443 distance: 97 - 102: 15.629 distance: 99 - 100: 28.445 distance: 99 - 101: 13.452 distance: 102 - 103: 23.745 distance: 103 - 104: 22.553 distance: 103 - 106: 6.443 distance: 104 - 105: 17.096 distance: 104 - 116: 16.897 distance: 106 - 107: 11.237 distance: 107 - 108: 10.435 distance: 107 - 109: 8.327 distance: 108 - 110: 3.958 distance: 109 - 111: 7.395 distance: 109 - 112: 13.317 distance: 110 - 111: 14.325 distance: 111 - 113: 5.316 distance: 113 - 115: 11.042 distance: 114 - 115: 7.245 distance: 116 - 117: 8.151 distance: 116 - 239: 20.100 distance: 117 - 118: 9.629 distance: 117 - 120: 20.874 distance: 118 - 119: 7.871 distance: 118 - 124: 3.775 distance: 119 - 236: 15.757 distance: 120 - 121: 18.764 distance: 121 - 122: 9.772 distance: 121 - 123: 20.185 distance: 124 - 125: 8.331 distance: 125 - 126: 6.599 distance: 125 - 128: 14.670 distance: 126 - 127: 13.739 distance: 126 - 131: 6.804 distance: 128 - 129: 7.013 distance: 128 - 130: 6.635 distance: 131 - 132: 4.031 distance: 131 - 226: 15.599 distance: 132 - 133: 7.203 distance: 132 - 135: 6.555 distance: 133 - 134: 18.971 distance: 133 - 140: 8.362 distance: 134 - 223: 19.703 distance: 135 - 136: 4.271 distance: 136 - 137: 9.641 distance: 137 - 138: 13.870 distance: 138 - 139: 10.583 distance: 140 - 141: 8.804 distance: 141 - 142: 15.685 distance: 142 - 144: 17.425 distance: 144 - 145: 7.526 distance: 144 - 214: 15.049 distance: 145 - 148: 9.342 distance: 146 - 147: 4.219 distance: 146 - 153: 7.174 distance: 147 - 211: 12.121 distance: 148 - 149: 20.014 distance: 149 - 150: 9.202 distance: 150 - 151: 16.497 distance: 150 - 152: 6.535 distance: 153 - 154: 6.925 distance: 154 - 157: 5.544 distance: 155 - 156: 4.631 distance: 155 - 165: 4.911 distance: 157 - 158: 16.449 distance: 158 - 160: 6.130 distance: 159 - 161: 8.595 distance: 160 - 162: 6.481 distance: 162 - 163: 7.474 distance: 165 - 198: 3.224 distance: 168 - 195: 3.027