Starting phenix.real_space_refine on Fri Aug 2 20:06:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h7z_34526/08_2024/8h7z_34526.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h7z_34526/08_2024/8h7z_34526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h7z_34526/08_2024/8h7z_34526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h7z_34526/08_2024/8h7z_34526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h7z_34526/08_2024/8h7z_34526.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h7z_34526/08_2024/8h7z_34526.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.105 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 22 5.16 5 C 3109 2.51 5 N 813 2.21 5 O 941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1": "OE1" <-> "OE2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I GLU 123": "OE1" <-> "OE2" Residue "I GLU 143": "OE1" <-> "OE2" 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: 4885 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1574 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 12, 'TRANS': 184} Chain: "F" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1685 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "I" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1626 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Time building chain proxies: 3.43, per 1000 atoms: 0.70 Number of scatterers: 4885 At special positions: 0 Unit cell: (66.8, 64.128, 134.936, 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 22 16.00 O 941 8.00 N 813 7.00 C 3109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 150 " - pdb=" SG CYS F 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 824.7 milliseconds 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 16 sheets defined 11.6% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.180A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.589A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.536A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.529A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.507A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.571A pdb=" N SER F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.967A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 139 No H-bonds generated for 'chain 'F' and resid 137 through 139' Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.692A pdb=" N ALA I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 Processing helix chain 'I' and resid 183 through 189 removed outlier: 3.525A pdb=" N LYS I 188 " --> pdb=" O ALA I 184 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS I 189 " --> pdb=" O ASP I 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.657A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.884A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.692A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.811A pdb=" N MET F 34 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.807A pdb=" N ARG F 98 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 133 through 134 removed outlier: 3.765A pdb=" N GLY F 149 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 133 through 134 removed outlier: 3.765A pdb=" N GLY F 149 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 153 through 155 Processing sheet with id=AB2, first strand: chain 'F' and resid 160 through 164 removed outlier: 3.661A pdb=" N VAL F 208 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL F 217 " --> pdb=" O VAL F 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS F 210 " --> pdb=" O THR F 215 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.662A pdb=" N GLU I 105 " --> pdb=" O MET I 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.497A pdb=" N TRP I 35 " --> pdb=" O ILE I 47 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLN I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET I 33 " --> pdb=" O GLN I 49 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 114 through 118 Processing sheet with id=AB7, first strand: chain 'I' and resid 153 through 155 removed outlier: 4.405A pdb=" N TRP I 148 " --> pdb=" O GLN I 155 " (cutoff:3.500A) 167 hydrogen bonds defined for protein. 423 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: 1.36 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1556 1.35 - 1.47: 1311 1.47 - 1.59: 2116 1.59 - 1.71: 0 1.71 - 1.83: 28 Bond restraints: 5011 Sorted by residual: bond pdb=" CA LYS I 24 " pdb=" C LYS I 24 " ideal model delta sigma weight residual 1.522 1.508 0.014 1.20e-02 6.94e+03 1.39e+00 bond pdb=" N ILE A 410 " pdb=" CA ILE A 410 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.20e+00 bond pdb=" CB LYS F 211 " pdb=" CG LYS F 211 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" CG PRO I 95 " pdb=" CD PRO I 95 " ideal model delta sigma weight residual 1.512 1.485 0.027 2.70e-02 1.37e+03 1.03e+00 bond pdb=" CG LYS F 211 " pdb=" CD LYS F 211 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.31e-01 ... (remaining 5006 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.99: 151 106.99 - 113.74: 2695 113.74 - 120.50: 1841 120.50 - 127.25: 2081 127.25 - 134.01: 49 Bond angle restraints: 6817 Sorted by residual: angle pdb=" N LYS F 153 " pdb=" CA LYS F 153 " pdb=" C LYS F 153 " ideal model delta sigma weight residual 108.69 115.32 -6.63 1.77e+00 3.19e-01 1.40e+01 angle pdb=" CB LYS F 211 " pdb=" CG LYS F 211 " pdb=" CD LYS F 211 " ideal model delta sigma weight residual 111.30 119.02 -7.72 2.30e+00 1.89e-01 1.13e+01 angle pdb=" N ASP F 154 " pdb=" CA ASP F 154 " pdb=" C ASP F 154 " ideal model delta sigma weight residual 110.80 117.76 -6.96 2.13e+00 2.20e-01 1.07e+01 angle pdb=" N LEU F 151 " pdb=" CA LEU F 151 " pdb=" C LEU F 151 " ideal model delta sigma weight residual 107.75 113.39 -5.64 1.86e+00 2.89e-01 9.20e+00 angle pdb=" N ILE I 48 " pdb=" CA ILE I 48 " pdb=" C ILE I 48 " ideal model delta sigma weight residual 108.48 112.63 -4.15 1.44e+00 4.82e-01 8.31e+00 ... (remaining 6812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 2691 15.79 - 31.58: 221 31.58 - 47.37: 56 47.37 - 63.15: 9 63.15 - 78.94: 4 Dihedral angle restraints: 2981 sinusoidal: 1145 harmonic: 1836 Sorted by residual: dihedral pdb=" CB CYS F 150 " pdb=" SG CYS F 150 " pdb=" SG CYS F 206 " pdb=" CB CYS F 206 " ideal model delta sinusoidal sigma weight residual -86.00 -118.96 32.96 1 1.00e+01 1.00e-02 1.54e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 65.21 27.79 1 1.00e+01 1.00e-02 1.11e+01 dihedral pdb=" CA CYS A 525 " pdb=" C CYS A 525 " pdb=" N GLY A 526 " pdb=" CA GLY A 526 " ideal model delta harmonic sigma weight residual -180.00 -163.45 -16.55 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 2978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 475 0.035 - 0.070: 185 0.070 - 0.105: 65 0.105 - 0.140: 21 0.140 - 0.175: 2 Chirality restraints: 748 Sorted by residual: chirality pdb=" CA ASP F 154 " pdb=" N ASP F 154 " pdb=" C ASP F 154 " pdb=" CB ASP F 154 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA VAL F 37 " pdb=" N VAL F 37 " pdb=" C VAL F 37 " pdb=" CB VAL F 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 745 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE I 46 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C PHE I 46 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE I 46 " -0.009 2.00e-02 2.50e+03 pdb=" N ILE I 47 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 46 " -0.009 2.00e-02 2.50e+03 8.91e-03 1.39e+00 pdb=" CG PHE I 46 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE I 46 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE I 46 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE I 46 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE I 46 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE I 46 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR I 14 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO I 15 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO I 15 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 15 " -0.016 5.00e-02 4.00e+02 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 392 2.75 - 3.29: 4504 3.29 - 3.82: 7513 3.82 - 4.36: 8931 4.36 - 4.90: 16163 Nonbonded interactions: 37503 Sorted by model distance: nonbonded pdb=" OG SER F 25 " pdb=" OE1 GLU F 26 " model vdw 2.210 3.040 nonbonded pdb=" NZ LYS I 18 " pdb=" OD1 ASN I 20 " model vdw 2.312 3.120 nonbonded pdb=" OG SER F 198 " pdb=" OH TYR F 204 " model vdw 2.341 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.348 3.040 nonbonded pdb=" N GLU I 79 " pdb=" OD2 ASP I 82 " model vdw 2.365 3.120 ... (remaining 37498 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=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: 3.230 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.790 Find NCS groups from input model: 0.070 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 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 0.032 5011 Z= 0.186 Angle : 0.633 7.723 6817 Z= 0.342 Chirality : 0.044 0.175 748 Planarity : 0.004 0.029 880 Dihedral : 12.594 78.942 1785 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.04 (0.35), residues: 625 helix: -2.16 (0.85), residues: 37 sheet: 1.28 (0.33), residues: 244 loop : -0.78 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 353 HIS 0.004 0.001 HIS F 35 PHE 0.021 0.001 PHE I 46 TYR 0.013 0.001 TYR A 495 ARG 0.002 0.000 ARG I 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: F 19 ARG cc_start: 0.8179 (ttm170) cc_final: 0.7507 (ttt180) REVERT: F 130 SER cc_start: 0.7070 (m) cc_final: 0.6704 (p) REVERT: I 42 GLU cc_start: 0.7574 (mp0) cc_final: 0.7230 (mp0) REVERT: I 122 ASP cc_start: 0.6882 (p0) cc_final: 0.6534 (p0) REVERT: I 123 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7194 (tt0) REVERT: I 170 ASP cc_start: 0.6762 (p0) cc_final: 0.6459 (p0) REVERT: I 179 LEU cc_start: 0.6648 (tp) cc_final: 0.6369 (tp) REVERT: I 199 GLN cc_start: 0.8528 (pt0) cc_final: 0.8048 (pm20) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2040 time to fit residues: 28.2870 Evaluate side-chains 69 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 0.0060 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 202 GLN I 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5011 Z= 0.191 Angle : 0.607 7.487 6817 Z= 0.315 Chirality : 0.045 0.142 748 Planarity : 0.004 0.040 880 Dihedral : 4.274 15.704 685 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.22 % Allowed : 7.02 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.07 (0.35), residues: 625 helix: -2.09 (0.91), residues: 32 sheet: 1.38 (0.33), residues: 245 loop : -0.95 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS F 35 PHE 0.028 0.002 PHE I 46 TYR 0.011 0.001 TYR I 140 ARG 0.003 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 19 ARG cc_start: 0.8299 (ttm170) cc_final: 0.7618 (ttt180) REVERT: F 130 SER cc_start: 0.7268 (m) cc_final: 0.6954 (p) outliers start: 12 outliers final: 10 residues processed: 81 average time/residue: 0.1857 time to fit residues: 19.1061 Evaluate side-chains 74 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 208 SER 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: 57.7533 > 50: distance: 18 - 104: 29.897 distance: 21 - 101: 7.231 distance: 44 - 48: 24.892 distance: 47 - 100: 32.129 distance: 48 - 49: 16.368 distance: 49 - 50: 10.781 distance: 49 - 52: 30.909 distance: 50 - 51: 8.304 distance: 50 - 56: 18.396 distance: 52 - 53: 16.359 distance: 53 - 54: 25.369 distance: 53 - 55: 14.064 distance: 56 - 57: 17.429 distance: 57 - 58: 14.646 distance: 58 - 59: 8.396 distance: 58 - 60: 4.718 distance: 60 - 61: 5.937 distance: 61 - 62: 11.107 distance: 61 - 64: 6.680 distance: 62 - 63: 16.281 distance: 62 - 67: 12.794 distance: 64 - 65: 10.279 distance: 64 - 66: 7.405 distance: 67 - 68: 18.484 distance: 68 - 69: 16.041 distance: 68 - 71: 16.607 distance: 69 - 70: 23.732 distance: 69 - 72: 18.500 distance: 72 - 73: 20.357 distance: 73 - 74: 35.167 distance: 74 - 75: 41.534 distance: 74 - 76: 15.383 distance: 76 - 77: 14.386 distance: 77 - 78: 5.495 distance: 77 - 80: 6.638 distance: 78 - 79: 19.341 distance: 78 - 87: 14.565 distance: 80 - 81: 13.491 distance: 81 - 82: 4.559 distance: 81 - 83: 8.397 distance: 82 - 84: 4.539 distance: 83 - 85: 8.920 distance: 84 - 86: 3.920 distance: 85 - 86: 5.611 distance: 87 - 88: 5.230 distance: 88 - 89: 9.440 distance: 88 - 91: 16.260 distance: 89 - 90: 7.435 distance: 89 - 95: 10.428 distance: 91 - 92: 9.590 distance: 92 - 93: 14.423 distance: 92 - 94: 12.687 distance: 95 - 96: 10.120 distance: 96 - 97: 19.435 distance: 96 - 99: 9.473 distance: 97 - 98: 30.066 distance: 97 - 101: 22.799 distance: 99 - 100: 39.523 distance: 101 - 102: 5.426 distance: 102 - 103: 7.139 distance: 102 - 105: 4.682 distance: 103 - 104: 35.924 distance: 103 - 113: 20.436 distance: 105 - 106: 22.597 distance: 106 - 107: 3.641 distance: 106 - 108: 11.013 distance: 107 - 109: 7.928 distance: 108 - 110: 9.025 distance: 109 - 111: 3.429 distance: 110 - 111: 8.124 distance: 113 - 114: 22.554 distance: 114 - 115: 34.082 distance: 114 - 117: 17.217 distance: 115 - 116: 20.104 distance: 115 - 124: 23.637 distance: 117 - 118: 31.974 distance: 118 - 119: 20.475 distance: 118 - 120: 23.308 distance: 119 - 121: 21.267 distance: 120 - 122: 12.413 distance: 121 - 123: 8.397 distance: 122 - 123: 8.162