Starting phenix.real_space_refine on Tue Apr 29 23:54:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jul_61829/04_2025/9jul_61829.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jul_61829/04_2025/9jul_61829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jul_61829/04_2025/9jul_61829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jul_61829/04_2025/9jul_61829.map" model { file = "/net/cci-nas-00/data/ceres_data/9jul_61829/04_2025/9jul_61829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jul_61829/04_2025/9jul_61829.cif" } resolution = 3.1 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= 0.002 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 41 5.16 5 C 5764 2.51 5 N 1543 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9005 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 8971 Classifications: {'peptide': 1165} Link IDs: {'PTRANS': 30, 'TRANS': 1134} Chain breaks: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'BLD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.53, per 1000 atoms: 0.61 Number of scatterers: 9005 At special positions: 0 Unit cell: (106.95, 99.51, 127.41, 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 41 16.00 O 1657 8.00 N 1543 7.00 C 5764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 3 sheets defined 69.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 37 through 75 removed outlier: 4.229A pdb=" N LEU A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 78 through 132 Processing helix chain 'A' and resid 134 through 141 removed outlier: 3.674A pdb=" N PHE A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 164 removed outlier: 4.309A pdb=" N VAL A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 187 Processing helix chain 'A' and resid 187 through 236 Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 245 through 299 Processing helix chain 'A' and resid 303 through 347 Proline residue: A 326 - end of helix removed outlier: 3.503A pdb=" N HIS A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 removed outlier: 3.782A pdb=" N VAL A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 413 " --> pdb=" O LYS A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 removed outlier: 4.253A pdb=" N LYS A 438 " --> pdb=" O LYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.529A pdb=" N ALA A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 522 Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.835A pdb=" N GLU A 542 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 696 through 729 removed outlier: 3.650A pdb=" N TYR A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 787 removed outlier: 4.178A pdb=" N SER A 752 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 787 " --> pdb=" O ALA A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 794 Processing helix chain 'A' and resid 799 through 852 removed outlier: 3.537A pdb=" N ALA A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL A 813 " --> pdb=" O ASP A 809 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 828 " --> pdb=" O ILE A 824 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ARG A 844 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 852 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 869 Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 878 through 891 Processing helix chain 'A' and resid 891 through 898 Processing helix chain 'A' and resid 900 through 954 Proline residue: A 914 - end of helix Processing helix chain 'A' and resid 958 through 981 Processing helix chain 'A' and resid 985 through 1001 Processing helix chain 'A' and resid 1064 through 1073 removed outlier: 3.536A pdb=" N VAL A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE A1069 " --> pdb=" O LYS A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1100 removed outlier: 3.762A pdb=" N LYS A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1122 Processing helix chain 'A' and resid 1129 through 1139 Processing helix chain 'A' and resid 1141 through 1148 removed outlier: 3.849A pdb=" N ALA A1147 " --> pdb=" O LYS A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1154 removed outlier: 3.705A pdb=" N THR A1154 " --> pdb=" O GLY A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1179 removed outlier: 3.593A pdb=" N ARG A1179 " --> pdb=" O ARG A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1210 Processing helix chain 'A' and resid 1234 through 1237 Processing helix chain 'A' and resid 1243 through 1250 removed outlier: 4.003A pdb=" N ASN A1250 " --> pdb=" O HIS A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1264 Processing sheet with id=AA1, first strand: chain 'A' and resid 447 through 448 removed outlier: 6.410A pdb=" N GLY A 447 " --> pdb=" O LEU A 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1042 through 1048 removed outlier: 4.347A pdb=" N ILE A1029 " --> pdb=" O ASP A1044 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N SER A1046 " --> pdb=" O LYS A1027 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LYS A1027 " --> pdb=" O SER A1046 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG A1048 " --> pdb=" O GLU A1025 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU A1025 " --> pdb=" O ARG A1048 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1102 through 1104 removed outlier: 7.096A pdb=" N ALA A1103 " --> pdb=" O LEU A1185 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N MET A1184 " --> pdb=" O ILE A1215 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL A1217 " --> pdb=" O MET A1184 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU A1186 " --> pdb=" O VAL A1217 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A1229 " --> pdb=" O THR A1054 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1812 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: 3.33 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1619 1.32 - 1.45: 2245 1.45 - 1.57: 5242 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 9174 Sorted by residual: bond pdb=" N PHE A 243 " pdb=" CA PHE A 243 " ideal model delta sigma weight residual 1.457 1.487 -0.030 6.40e-03 2.44e+04 2.22e+01 bond pdb=" N VAL A1058 " pdb=" CA VAL A1058 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.15e-02 7.56e+03 9.65e+00 bond pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 8.72e+00 bond pdb=" N VAL A 198 " pdb=" CA VAL A 198 " ideal model delta sigma weight residual 1.463 1.498 -0.035 1.20e-02 6.94e+03 8.36e+00 bond pdb=" N ILE A1039 " pdb=" CA ILE A1039 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.25e+00 ... (remaining 9169 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 11716 1.61 - 3.21: 633 3.21 - 4.82: 59 4.82 - 6.42: 15 6.42 - 8.03: 2 Bond angle restraints: 12425 Sorted by residual: angle pdb=" C PHE A 243 " pdb=" CA PHE A 243 " pdb=" CB PHE A 243 " ideal model delta sigma weight residual 117.07 111.28 5.79 1.44e+00 4.82e-01 1.62e+01 angle pdb=" CA LEU A1026 " pdb=" C LEU A1026 " pdb=" O LEU A1026 " ideal model delta sigma weight residual 122.64 117.85 4.79 1.25e+00 6.40e-01 1.47e+01 angle pdb=" N PHE A1075 " pdb=" CA PHE A1075 " pdb=" C PHE A1075 " ideal model delta sigma weight residual 111.28 107.30 3.98 1.09e+00 8.42e-01 1.34e+01 angle pdb=" N GLN A1073 " pdb=" CA GLN A1073 " pdb=" C GLN A1073 " ideal model delta sigma weight residual 113.20 109.00 4.20 1.21e+00 6.83e-01 1.21e+01 angle pdb=" O PHE A 243 " pdb=" C PHE A 243 " pdb=" N VAL A 244 " ideal model delta sigma weight residual 121.47 124.07 -2.60 7.50e-01 1.78e+00 1.20e+01 ... (remaining 12420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5006 17.59 - 35.18: 425 35.18 - 52.77: 71 52.77 - 70.36: 41 70.36 - 87.96: 5 Dihedral angle restraints: 5548 sinusoidal: 2194 harmonic: 3354 Sorted by residual: dihedral pdb=" CA VAL A 156 " pdb=" C VAL A 156 " pdb=" N MET A 157 " pdb=" CA MET A 157 " ideal model delta harmonic sigma weight residual -180.00 -160.64 -19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA LEU A 982 " pdb=" C LEU A 982 " pdb=" N ALA A 983 " pdb=" CA ALA A 983 " ideal model delta harmonic sigma weight residual -180.00 -162.75 -17.25 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA PRO A 525 " pdb=" C PRO A 525 " pdb=" N ALA A 526 " pdb=" CA ALA A 526 " ideal model delta harmonic sigma weight residual 180.00 164.37 15.63 0 5.00e+00 4.00e-02 9.78e+00 ... (remaining 5545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1178 0.064 - 0.129: 208 0.129 - 0.193: 47 0.193 - 0.257: 6 0.257 - 0.321: 2 Chirality restraints: 1441 Sorted by residual: chirality pdb=" C10 BLD A1301 " pdb=" C01 BLD A1301 " pdb=" C05 BLD A1301 " pdb=" C09 BLD A1301 " both_signs ideal model delta sigma weight residual False -3.02 -2.70 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C08 BLD A1301 " pdb=" C07 BLD A1301 " pdb=" C09 BLD A1301 " pdb=" C14 BLD A1301 " both_signs ideal model delta sigma weight residual False 2.71 2.44 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C23 BLD A1301 " pdb=" C22 BLD A1301 " pdb=" C24 BLD A1301 " pdb=" O23 BLD A1301 " both_signs ideal model delta sigma weight residual False -2.29 -2.53 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 1438 not shown) Planarity restraints: 1573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 238 " 0.218 9.50e-02 1.11e+02 9.77e-02 5.87e+00 pdb=" NE ARG A 238 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 238 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 238 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 238 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 705 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.44e+00 pdb=" C VAL A 705 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL A 705 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 706 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 721 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C LEU A 721 " -0.032 2.00e-02 2.50e+03 pdb=" O LEU A 721 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 722 " 0.011 2.00e-02 2.50e+03 ... (remaining 1570 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1654 2.77 - 3.30: 9829 3.30 - 3.84: 15542 3.84 - 4.37: 18034 4.37 - 4.90: 30048 Nonbonded interactions: 75107 Sorted by model distance: nonbonded pdb=" O SER A 704 " pdb=" OG SER A 707 " model vdw 2.238 3.040 nonbonded pdb=" O ALA A1130 " pdb=" NE2 GLN A1134 " model vdw 2.258 3.120 nonbonded pdb=" O GLY A1123 " pdb=" NH1 ARG A1179 " model vdw 2.277 3.120 nonbonded pdb=" O ARG A1220 " pdb=" OG1 THR A1223 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASP A1089 " pdb=" N ARG A1091 " model vdw 2.313 3.120 ... (remaining 75102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.780 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.340 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 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 : 0.005 0.063 9174 Z= 0.369 Angle : 0.757 8.030 12425 Z= 0.511 Chirality : 0.055 0.321 1441 Planarity : 0.006 0.098 1573 Dihedral : 14.486 87.955 3390 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.74 % Allowed : 1.05 % Favored : 98.21 % 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: 0.64 (0.25), residues: 1161 helix: 1.62 (0.19), residues: 754 sheet: -0.30 (0.96), residues: 25 loop : -2.07 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 697 HIS 0.006 0.001 HIS A 171 PHE 0.021 0.002 PHE A 72 TYR 0.015 0.001 TYR A 938 ARG 0.010 0.001 ARG A 801 Details of bonding type rmsd hydrogen bonds : bond 0.13394 ( 616) hydrogen bonds : angle 5.41651 ( 1812) covalent geometry : bond 0.00542 ( 9174) covalent geometry : angle 0.75728 (12425) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8176 (mtp) REVERT: A 432 GLN cc_start: 0.7998 (mp10) cc_final: 0.7532 (mp10) REVERT: A 465 LEU cc_start: 0.9112 (mm) cc_final: 0.8827 (mm) REVERT: A 492 LEU cc_start: 0.7901 (tp) cc_final: 0.7626 (tp) REVERT: A 553 MET cc_start: 0.7270 (pmm) cc_final: 0.7047 (pmm) REVERT: A 970 MET cc_start: 0.8999 (mmt) cc_final: 0.8361 (mmt) outliers start: 7 outliers final: 1 residues processed: 155 average time/residue: 0.3244 time to fit residues: 66.4481 Evaluate side-chains 119 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 1042 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.8857 > 50: distance: 71 - 93: 7.186 distance: 76 - 99: 13.905 distance: 80 - 85: 6.419 distance: 81 - 107: 17.432 distance: 85 - 86: 4.209 distance: 86 - 87: 4.064 distance: 86 - 89: 9.895 distance: 87 - 88: 14.180 distance: 87 - 93: 6.774 distance: 88 - 115: 22.720 distance: 89 - 90: 5.174 distance: 89 - 91: 19.878 distance: 90 - 92: 15.052 distance: 93 - 94: 13.071 distance: 94 - 95: 19.809 distance: 94 - 97: 7.824 distance: 95 - 96: 15.786 distance: 95 - 99: 11.663 distance: 97 - 98: 5.713 distance: 99 - 100: 14.803 distance: 100 - 101: 23.005 distance: 100 - 103: 5.339 distance: 101 - 102: 22.065 distance: 101 - 107: 19.186 distance: 103 - 104: 24.684 distance: 104 - 105: 4.899 distance: 104 - 106: 37.376 distance: 107 - 108: 17.512 distance: 108 - 109: 12.495 distance: 108 - 111: 13.867 distance: 109 - 110: 12.465 distance: 109 - 115: 7.056 distance: 111 - 112: 24.221 distance: 111 - 113: 12.638 distance: 112 - 114: 33.827 distance: 115 - 116: 20.828 distance: 116 - 117: 13.122 distance: 116 - 119: 7.542 distance: 117 - 118: 18.022 distance: 117 - 124: 13.345 distance: 119 - 120: 24.817 distance: 120 - 121: 21.923 distance: 121 - 122: 6.010 distance: 121 - 123: 8.912 distance: 124 - 125: 8.521 distance: 125 - 126: 9.655 distance: 125 - 128: 10.730 distance: 126 - 127: 24.456 distance: 126 - 135: 26.216 distance: 128 - 129: 14.891 distance: 129 - 130: 14.551 distance: 130 - 131: 23.336 distance: 131 - 132: 17.533 distance: 132 - 133: 20.051 distance: 132 - 134: 6.606 distance: 135 - 136: 12.195 distance: 136 - 137: 24.981 distance: 136 - 139: 16.197 distance: 137 - 138: 35.086 distance: 137 - 146: 20.655 distance: 139 - 140: 14.815 distance: 140 - 141: 32.462 distance: 140 - 142: 13.688 distance: 141 - 143: 35.646 distance: 142 - 144: 38.995 distance: 143 - 145: 38.570 distance: 146 - 147: 8.631 distance: 147 - 148: 11.467 distance: 147 - 150: 41.540 distance: 148 - 149: 10.284 distance: 148 - 158: 28.278 distance: 150 - 151: 16.398 distance: 151 - 152: 5.775 distance: 151 - 153: 3.579 distance: 152 - 154: 27.244 distance: 153 - 155: 15.013 distance: 154 - 156: 17.031 distance: 155 - 156: 15.949 distance: 156 - 157: 18.385 distance: 158 - 159: 19.168 distance: 159 - 160: 21.489 distance: 160 - 161: 21.500 distance: 160 - 167: 14.228 distance: 162 - 163: 46.457 distance: 163 - 164: 21.271 distance: 164 - 165: 19.074 distance: 164 - 166: 30.936 distance: 167 - 168: 5.042 distance: 167 - 173: 34.124 distance: 168 - 169: 19.769 distance: 168 - 171: 10.001 distance: 169 - 170: 39.400 distance: 169 - 174: 22.810 distance: 171 - 172: 44.531 distance: 172 - 173: 28.348