Starting phenix.real_space_refine on Fri Aug 2 19:11:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tth_41608/08_2024/8tth_41608.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tth_41608/08_2024/8tth_41608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tth_41608/08_2024/8tth_41608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tth_41608/08_2024/8tth_41608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tth_41608/08_2024/8tth_41608.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tth_41608/08_2024/8tth_41608.cif" } resolution = 3.54 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= 0.002 sd= 0.060 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 26 5.16 5 C 3031 2.51 5 N 729 2.21 5 O 834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 63": "OD1" <-> "OD2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 41": "OD1" <-> "OD2" Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 106": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4620 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2842 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Chain: "C" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "D" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Time building chain proxies: 3.38, per 1000 atoms: 0.73 Number of scatterers: 4620 At special positions: 0 Unit cell: (60.225, 72.6, 106.425, 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 26 16.00 O 834 8.00 N 729 7.00 C 3031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 122 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 829.4 milliseconds 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1092 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 6 sheets defined 58.7% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 2 through 33 removed outlier: 3.715A pdb=" N PHE A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 15 " --> pdb=" O ASN A 11 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Proline residue: A 24 - end of helix Proline residue: A 27 - end of helix removed outlier: 3.917A pdb=" N LEU A 33 " --> pdb=" O TYR A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 66 removed outlier: 3.666A pdb=" N LEU A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Proline residue: A 56 - end of helix Processing helix chain 'A' and resid 66 through 86 removed outlier: 3.837A pdb=" N ALA A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 120 Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 125 through 150 Proline residue: A 144 - end of helix removed outlier: 3.931A pdb=" N MET A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 177 removed outlier: 3.543A pdb=" N VAL A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 233 removed outlier: 4.009A pdb=" N SER A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 266 removed outlier: 4.022A pdb=" N ILE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LYS A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 289 removed outlier: 3.996A pdb=" N LEU A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 322 removed outlier: 3.639A pdb=" N ILE A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 324 through 354 Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 356 through 382 Processing helix chain 'C' and resid 54 through 56 No H-bonds generated for 'chain 'C' and resid 54 through 56' Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 103 through 107 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 33 Processing sheet with id=AA2, first strand: chain 'C' and resid 36 through 37 removed outlier: 8.450A pdb=" N ASP C 144 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N SER C 126 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TRP C 146 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ARG C 124 " --> pdb=" O TRP C 146 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN C 148 " --> pdb=" O CYS C 122 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS C 122 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG C 64 " --> pdb=" O TRP C 73 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP C 73 " --> pdb=" O ARG C 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AA4, first strand: chain 'D' and resid 28 through 31 Processing sheet with id=AA5, first strand: chain 'D' and resid 34 through 36 removed outlier: 3.663A pdb=" N LEU D 35 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP D 59 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 34 through 36 removed outlier: 3.663A pdb=" N LEU D 35 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN D 114 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR D 121 " --> pdb=" O GLN D 114 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 915 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: 1.29 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1398 1.34 - 1.46: 1212 1.46 - 1.58: 2078 1.58 - 1.70: 0 1.70 - 1.81: 47 Bond restraints: 4735 Sorted by residual: bond pdb=" CA MET A 150 " pdb=" CB MET A 150 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.35e-02 5.49e+03 1.60e+00 bond pdb=" C GLN D 103 " pdb=" O GLN D 103 " ideal model delta sigma weight residual 1.236 1.246 -0.010 8.90e-03 1.26e+04 1.22e+00 bond pdb=" CA PHE C 134 " pdb=" CB PHE C 134 " ideal model delta sigma weight residual 1.535 1.548 -0.013 1.37e-02 5.33e+03 8.91e-01 bond pdb=" C LEU D 102 " pdb=" N GLN D 103 " ideal model delta sigma weight residual 1.326 1.335 -0.009 1.12e-02 7.97e+03 7.17e-01 bond pdb=" CB ASN C 110 " pdb=" CG ASN C 110 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.96e-01 ... (remaining 4730 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.91: 127 106.91 - 113.71: 2569 113.71 - 120.52: 1908 120.52 - 127.32: 1773 127.32 - 134.13: 45 Bond angle restraints: 6422 Sorted by residual: angle pdb=" N VAL D 53 " pdb=" CA VAL D 53 " pdb=" C VAL D 53 " ideal model delta sigma weight residual 113.53 108.33 5.20 9.80e-01 1.04e+00 2.82e+01 angle pdb=" C TYR C 133 " pdb=" N PHE C 134 " pdb=" CA PHE C 134 " ideal model delta sigma weight residual 125.02 130.27 -5.25 1.76e+00 3.23e-01 8.89e+00 angle pdb=" CA LEU A 42 " pdb=" CB LEU A 42 " pdb=" CG LEU A 42 " ideal model delta sigma weight residual 116.30 125.98 -9.68 3.50e+00 8.16e-02 7.64e+00 angle pdb=" CB MET A 150 " pdb=" CG MET A 150 " pdb=" SD MET A 150 " ideal model delta sigma weight residual 112.70 120.88 -8.18 3.00e+00 1.11e-01 7.43e+00 angle pdb=" N LEU D 35 " pdb=" CA LEU D 35 " pdb=" C LEU D 35 " ideal model delta sigma weight residual 107.23 111.65 -4.42 1.67e+00 3.59e-01 7.00e+00 ... (remaining 6417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 2339 17.62 - 35.23: 314 35.23 - 52.84: 67 52.84 - 70.46: 19 70.46 - 88.07: 1 Dihedral angle restraints: 2740 sinusoidal: 1021 harmonic: 1719 Sorted by residual: dihedral pdb=" CB CYS D 47 " pdb=" SG CYS D 47 " pdb=" SG CYS D 112 " pdb=" CB CYS D 112 " ideal model delta sinusoidal sigma weight residual -86.00 -32.52 -53.48 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CA TRP C 131 " pdb=" C TRP C 131 " pdb=" N TYR C 132 " pdb=" CA TYR C 132 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA MET A 150 " pdb=" C MET A 150 " pdb=" N ALA A 151 " pdb=" CA ALA A 151 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 2737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 520 0.040 - 0.079: 156 0.079 - 0.119: 49 0.119 - 0.158: 6 0.158 - 0.198: 3 Chirality restraints: 734 Sorted by residual: chirality pdb=" CG LEU A 49 " pdb=" CB LEU A 49 " pdb=" CD1 LEU A 49 " pdb=" CD2 LEU A 49 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.80e-01 chirality pdb=" CA PHE C 134 " pdb=" N PHE C 134 " pdb=" C PHE C 134 " pdb=" CB PHE C 134 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CB VAL C 90 " pdb=" CA VAL C 90 " pdb=" CG1 VAL C 90 " pdb=" CG2 VAL C 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 731 not shown) Planarity restraints: 792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 103 " 0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO D 104 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 104 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 104 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 236 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO A 237 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 157 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO A 158 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 158 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 158 " 0.019 5.00e-02 4.00e+02 ... (remaining 789 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 179 2.72 - 3.26: 4770 3.26 - 3.81: 7840 3.81 - 4.35: 8833 4.35 - 4.90: 15676 Nonbonded interactions: 37298 Sorted by model distance: nonbonded pdb=" OE1 GLN D 30 " pdb=" OG1 THR D 126 " model vdw 2.174 3.040 nonbonded pdb=" OH TYR D 60 " pdb=" OE1 GLN D 113 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR A 278 " pdb=" O VAL A 301 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR A 29 " pdb=" O HIS A 155 " model vdw 2.296 3.040 nonbonded pdb=" O PHE C 55 " pdb=" OG SER C 79 " model vdw 2.311 3.040 ... (remaining 37293 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.560 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.210 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 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 : 0.003 0.024 4735 Z= 0.171 Angle : 0.687 9.675 6422 Z= 0.369 Chirality : 0.043 0.198 734 Planarity : 0.004 0.040 792 Dihedral : 16.672 88.074 1642 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.20 % Allowed : 31.00 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.88 (0.36), residues: 595 helix: 1.66 (0.30), residues: 323 sheet: 0.34 (0.51), residues: 109 loop : -1.40 (0.51), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.018 0.002 PHE C 134 TYR 0.012 0.001 TYR D 73 ARG 0.002 0.000 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: C 61 HIS cc_start: 0.8230 (m170) cc_final: 0.7925 (m170) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1310 time to fit residues: 22.8679 Evaluate side-chains 125 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 0.0770 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4735 Z= 0.194 Angle : 0.617 6.754 6422 Z= 0.319 Chirality : 0.043 0.215 734 Planarity : 0.005 0.041 792 Dihedral : 5.109 64.691 643 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.20 % Allowed : 27.60 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.20 (0.37), residues: 595 helix: 1.85 (0.30), residues: 324 sheet: 0.36 (0.50), residues: 112 loop : -1.06 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.022 0.002 PHE C 134 TYR 0.016 0.001 TYR C 133 ARG 0.002 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 74 SER cc_start: 0.7652 (p) cc_final: 0.7400 (p) outliers start: 21 outliers final: 12 residues processed: 144 average time/residue: 0.1310 time to fit residues: 25.2146 Evaluate side-chains 137 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain D residue 112 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 0.0170 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 0.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4735 Z= 0.201 Angle : 0.601 8.557 6422 Z= 0.311 Chirality : 0.043 0.217 734 Planarity : 0.004 0.046 792 Dihedral : 5.032 59.657 643 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.00 % Allowed : 28.20 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.09 (0.36), residues: 595 helix: 1.70 (0.30), residues: 328 sheet: 0.36 (0.51), residues: 110 loop : -1.04 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 62 HIS 0.004 0.001 HIS A 155 PHE 0.020 0.002 PHE C 134 TYR 0.014 0.002 TYR C 133 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8684 (mm) cc_final: 0.8480 (mm) REVERT: A 68 LYS cc_start: 0.7723 (pttm) cc_final: 0.7399 (pttt) REVERT: C 106 TYR cc_start: 0.7143 (m-80) cc_final: 0.6202 (m-80) REVERT: C 109 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6554 (mmt) REVERT: D 73 TYR cc_start: 0.7813 (p90) cc_final: 0.7397 (p90) outliers start: 25 outliers final: 18 residues processed: 147 average time/residue: 0.1289 time to fit residues: 25.1603 Evaluate side-chains 146 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 67.057 > 50: distance: 69 - 158: 29.709 distance: 86 - 144: 33.212 distance: 89 - 141: 25.386 distance: 111 - 116: 30.095 distance: 116 - 117: 14.376 distance: 117 - 118: 36.049 distance: 118 - 119: 31.271 distance: 118 - 120: 10.149 distance: 120 - 121: 16.124 distance: 121 - 122: 22.794 distance: 121 - 124: 36.008 distance: 122 - 123: 7.439 distance: 122 - 129: 42.230 distance: 124 - 125: 18.975 distance: 125 - 126: 38.694 distance: 126 - 127: 45.440 distance: 127 - 128: 23.349 distance: 129 - 130: 33.618 distance: 130 - 131: 37.485 distance: 130 - 133: 40.676 distance: 134 - 135: 41.041 distance: 134 - 140: 33.230 distance: 135 - 136: 28.715 distance: 135 - 138: 37.669 distance: 136 - 137: 13.489 distance: 136 - 141: 27.070 distance: 138 - 139: 9.604 distance: 139 - 140: 26.812 distance: 141 - 142: 5.039 distance: 142 - 143: 11.272 distance: 142 - 145: 15.989 distance: 143 - 144: 3.520 distance: 143 - 150: 15.158 distance: 145 - 146: 28.944 distance: 146 - 147: 10.859 distance: 147 - 148: 7.943 distance: 148 - 149: 36.263 distance: 150 - 151: 29.952 distance: 151 - 152: 31.385 distance: 151 - 154: 38.316 distance: 152 - 153: 7.079 distance: 152 - 158: 16.091 distance: 154 - 155: 22.904 distance: 155 - 156: 15.424 distance: 155 - 157: 12.445 distance: 158 - 159: 9.643 distance: 159 - 160: 28.959 distance: 160 - 161: 13.350 distance: 160 - 166: 11.622 distance: 162 - 163: 19.303 distance: 163 - 164: 15.856 distance: 163 - 165: 16.593 distance: 166 - 167: 17.032 distance: 167 - 168: 17.447 distance: 167 - 170: 3.528 distance: 168 - 169: 18.687 distance: 168 - 174: 5.255 distance: 170 - 171: 36.754 distance: 170 - 172: 55.611 distance: 171 - 173: 40.648 distance: 174 - 175: 13.924 distance: 175 - 176: 14.113 distance: 175 - 178: 14.709 distance: 176 - 177: 18.628 distance: 176 - 186: 28.868 distance: 178 - 179: 6.116 distance: 179 - 181: 5.401 distance: 180 - 182: 6.267 distance: 181 - 183: 9.790 distance: 182 - 184: 5.710 distance: 183 - 184: 12.175 distance: 184 - 185: 12.155 distance: 186 - 187: 20.053 distance: 187 - 190: 11.889 distance: 188 - 189: 19.577 distance: 188 - 192: 27.607 distance: 190 - 191: 19.144