Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:51:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk6_25174/12_2022/7sk6_25174_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk6_25174/12_2022/7sk6_25174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk6_25174/12_2022/7sk6_25174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk6_25174/12_2022/7sk6_25174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk6_25174/12_2022/7sk6_25174_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk6_25174/12_2022/7sk6_25174_neut.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9144 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4799 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 11, 'TRANS': 288} Chain breaks: 1 Chain: "B" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 987 Classifications: {'peptide': 59} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1507 Classifications: {'peptide': 101} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "F" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1851 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Time building chain proxies: 4.71, per 1000 atoms: 0.52 Number of scatterers: 9144 At special positions: 0 Unit cell: (61.56, 66.96, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 O 833 8.00 N 766 7.00 C 3052 6.00 H 4462 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 34 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 50 " distance=2.02 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " 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: 6.89 Conformation dependent library (CDL) restraints added in 718.8 milliseconds 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1118 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 8 sheets defined 46.7% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 39 through 76 removed outlier: 3.837A pdb=" N PHE A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.748A pdb=" N LEU A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 106 removed outlier: 4.041A pdb=" N TRP A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 148 removed outlier: 4.074A pdb=" N TYR A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 182 Proline residue: A 178 - end of helix removed outlier: 3.519A pdb=" N TYR A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 221 Processing helix chain 'A' and resid 221 through 242 Processing helix chain 'A' and resid 244 through 249 removed outlier: 4.184A pdb=" N HIS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 280 removed outlier: 3.963A pdb=" N PHE A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 286 through 316 removed outlier: 3.719A pdb=" N HIS A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N CYS A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N CYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Proline residue: A 312 - end of helix removed outlier: 3.748A pdb=" N TYR A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 Processing helix chain 'B' and resid 2 through 7 removed outlier: 4.035A pdb=" N TYR B 7 " --> pdb=" O SER B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 65 Processing helix chain 'F' and resid 65 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 33 removed outlier: 3.510A pdb=" N VAL B 49 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 3.537A pdb=" N SER F 112 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 186 removed outlier: 3.734A pdb=" N TYR A 195 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AA5, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.754A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 6 through 10 removed outlier: 3.608A pdb=" N THR F 81 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 13 through 14 removed outlier: 5.985A pdb=" N GLY F 13 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA F 52 " --> pdb=" O TRP F 39 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 13 through 14 removed outlier: 5.985A pdb=" N GLY F 13 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR F 119 " --> pdb=" O ARG F 101 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 753 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: 3.24 Time building geometry restraints manager: 7.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4452 1.04 - 1.24: 594 1.24 - 1.43: 1575 1.43 - 1.63: 2607 1.63 - 1.83: 42 Bond restraints: 9270 Sorted by residual: bond pdb=" ND1 HIS A 248 " pdb=" CE1 HIS A 248 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.30e+01 bond pdb=" ND1 HIS A 107 " pdb=" CE1 HIS A 107 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.29e+01 bond pdb=" ND1 HIS A 269 " pdb=" CE1 HIS A 269 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.26e+01 bond pdb=" ND1 HIS A 203 " pdb=" CE1 HIS A 203 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.23e+01 bond pdb=" ND1 HIS A 291 " pdb=" CE1 HIS A 291 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.23e+01 ... (remaining 9265 not shown) Histogram of bond angle deviations from ideal: 91.98 - 100.35: 15 100.35 - 108.73: 3558 108.73 - 117.10: 8220 117.10 - 125.48: 4651 125.48 - 133.85: 172 Bond angle restraints: 16616 Sorted by residual: angle pdb=" CA ILE A 97 " pdb=" C ILE A 97 " pdb=" N PRO A 98 " ideal model delta sigma weight residual 120.83 125.23 -4.40 6.10e-01 2.69e+00 5.20e+01 angle pdb=" N LYS F 79 " pdb=" CA LYS F 79 " pdb=" C LYS F 79 " ideal model delta sigma weight residual 108.90 98.42 10.48 1.63e+00 3.76e-01 4.13e+01 angle pdb=" N VAL B 39 " pdb=" CA VAL B 39 " pdb=" C VAL B 39 " ideal model delta sigma weight residual 108.81 98.54 10.27 1.62e+00 3.81e-01 4.02e+01 angle pdb=" C ILE A 210 " pdb=" N GLY A 211 " pdb=" CA GLY A 211 " ideal model delta sigma weight residual 119.99 126.87 -6.88 1.13e+00 7.83e-01 3.70e+01 angle pdb=" C ILE A 205 " pdb=" N LYS A 206 " pdb=" CA LYS A 206 " ideal model delta sigma weight residual 120.79 129.21 -8.42 1.39e+00 5.18e-01 3.67e+01 ... (remaining 16611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 3685 17.49 - 34.97: 111 34.97 - 52.46: 21 52.46 - 69.95: 26 69.95 - 87.43: 4 Dihedral angle restraints: 3847 sinusoidal: 1691 harmonic: 2156 Sorted by residual: dihedral pdb=" N HIS A 281 " pdb=" C HIS A 281 " pdb=" CA HIS A 281 " pdb=" CB HIS A 281 " ideal model delta harmonic sigma weight residual 122.80 133.20 -10.40 0 2.50e+00 1.60e-01 1.73e+01 dihedral pdb=" CA THR A 147 " pdb=" C THR A 147 " pdb=" N TYR A 148 " pdb=" CA TYR A 148 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C ILE A 146 " pdb=" N ILE A 146 " pdb=" CA ILE A 146 " pdb=" CB ILE A 146 " ideal model delta harmonic sigma weight residual -122.00 -131.85 9.85 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 3844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 480 0.093 - 0.186: 203 0.186 - 0.279: 51 0.279 - 0.373: 10 0.373 - 0.466: 3 Chirality restraints: 747 Sorted by residual: chirality pdb=" CA HIS A 281 " pdb=" N HIS A 281 " pdb=" C HIS A 281 " pdb=" CB HIS A 281 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CA THR A 300 " pdb=" N THR A 300 " pdb=" C THR A 300 " pdb=" CB THR A 300 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CA ASN A 127 " pdb=" N ASN A 127 " pdb=" C ASN A 127 " pdb=" CB ASN A 127 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 744 not shown) Planarity restraints: 1351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 109 " -0.146 2.00e-02 2.50e+03 5.67e-02 1.29e+02 pdb=" CG TRP F 109 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP F 109 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP F 109 " 0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP F 109 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP F 109 " 0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP F 109 " 0.104 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 109 " -0.050 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 109 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 109 " -0.088 2.00e-02 2.50e+03 pdb=" HD1 TRP F 109 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP F 109 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP F 109 " 0.008 2.00e-02 2.50e+03 pdb=" HZ2 TRP F 109 " -0.006 2.00e-02 2.50e+03 pdb=" HZ3 TRP F 109 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP F 109 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 83 " 0.094 2.00e-02 2.50e+03 4.09e-02 5.01e+01 pdb=" CG TYR F 83 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR F 83 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR F 83 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR F 83 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR F 83 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR F 83 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 83 " 0.077 2.00e-02 2.50e+03 pdb=" HD1 TYR F 83 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR F 83 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR F 83 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR F 83 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 322 " -0.093 2.00e-02 2.50e+03 3.92e-02 4.62e+01 pdb=" CG TYR A 322 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 322 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 322 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 322 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR A 322 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 322 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 322 " -0.068 2.00e-02 2.50e+03 pdb=" HD1 TYR A 322 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 322 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TYR A 322 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 322 " 0.001 2.00e-02 2.50e+03 ... (remaining 1348 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 584 2.25 - 2.83: 19486 2.83 - 3.42: 24520 3.42 - 4.01: 32883 4.01 - 4.60: 49936 Nonbonded interactions: 127409 Sorted by model distance: nonbonded pdb=" H THR A 150 " pdb=" H ASN A 151 " model vdw 1.658 2.100 nonbonded pdb=" H ASN B 45 " pdb=" H ASN B 46 " model vdw 1.661 2.100 nonbonded pdb=" H ALA E 52 " pdb=" H SER E 53 " model vdw 1.689 2.100 nonbonded pdb=" H SER E 53 " pdb=" H SER E 54 " model vdw 1.705 2.100 nonbonded pdb=" H LYS B 54 " pdb=" H LEU B 55 " model vdw 1.727 2.100 ... (remaining 127404 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 31 5.16 5 C 3052 2.51 5 N 766 2.21 5 O 833 1.98 5 H 4462 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.810 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: 0.130 Extract box with map and model: 7.540 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.070 Process input model: 31.980 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5154 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 : 0.018 0.045 4808 Z= 1.167 Angle : 1.923 10.476 6545 Z= 1.309 Chirality : 0.111 0.466 747 Planarity : 0.014 0.089 796 Dihedral : 13.164 87.433 1684 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 0.21 Ramachandran Plot: Outliers : 1.75 % Allowed : 4.20 % Favored : 94.05 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 8.70 % 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: 0.35 (0.36), residues: 571 helix: 2.83 (0.32), residues: 245 sheet: -1.42 (0.46), residues: 117 loop : -2.05 (0.36), residues: 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 112 average time/residue: 0.3981 time to fit residues: 55.4387 Evaluate side-chains 79 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.760 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3349 time to fit residues: 1.8126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 245 GLN F 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5327 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4808 Z= 0.198 Angle : 0.610 4.964 6545 Z= 0.341 Chirality : 0.043 0.168 747 Planarity : 0.005 0.042 796 Dihedral : 5.310 25.479 638 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.68 % Favored : 96.15 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.56 (0.35), residues: 571 helix: 2.70 (0.31), residues: 245 sheet: -1.20 (0.48), residues: 113 loop : -1.59 (0.37), residues: 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 81 average time/residue: 0.3214 time to fit residues: 33.9165 Evaluate side-chains 76 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.772 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1188 time to fit residues: 2.1945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 GLN E 4 GLN E 7 GLN F 16 GLN F 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5618 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 4808 Z= 0.332 Angle : 0.648 5.246 6545 Z= 0.365 Chirality : 0.043 0.167 747 Planarity : 0.005 0.036 796 Dihedral : 5.406 26.391 638 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.15 (0.34), residues: 571 helix: 1.93 (0.31), residues: 245 sheet: -1.58 (0.48), residues: 111 loop : -1.68 (0.37), residues: 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 74 average time/residue: 0.3123 time to fit residues: 30.4781 Evaluate side-chains 72 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.891 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1194 time to fit residues: 2.7352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 GLN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5774 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 4808 Z= 0.374 Angle : 0.662 5.282 6545 Z= 0.374 Chirality : 0.042 0.150 747 Planarity : 0.005 0.044 796 Dihedral : 5.594 27.192 638 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.74 (0.34), residues: 571 helix: 1.49 (0.31), residues: 244 sheet: -2.05 (0.48), residues: 106 loop : -1.96 (0.37), residues: 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 63 average time/residue: 0.2934 time to fit residues: 25.0100 Evaluate side-chains 61 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.699 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1408 time to fit residues: 1.7806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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: 59.4784 > 50: distance: 18 - 226: 6.402 distance: 21 - 264: 5.029 distance: 42 - 267: 3.839 distance: 45 - 297: 7.969 distance: 186 - 358: 6.746 distance: 208 - 223: 9.277 distance: 223 - 224: 4.536 distance: 223 - 231: 9.117 distance: 224 - 225: 6.111 distance: 224 - 227: 4.659 distance: 224 - 232: 10.230 distance: 225 - 226: 4.333 distance: 225 - 242: 8.986 distance: 227 - 233: 5.540 distance: 227 - 234: 4.809 distance: 228 - 229: 3.730 distance: 228 - 230: 3.837 distance: 230 - 241: 3.758 distance: 242 - 243: 9.021 distance: 242 - 251: 22.867 distance: 242 - 424: 13.093 distance: 243 - 244: 3.722 distance: 243 - 246: 5.535 distance: 243 - 252: 12.365 distance: 244 - 245: 5.356 distance: 244 - 264: 3.395 distance: 245 - 421: 10.683 distance: 246 - 247: 4.971 distance: 246 - 253: 9.138 distance: 246 - 254: 4.769 distance: 247 - 248: 4.356 distance: 247 - 255: 3.620 distance: 247 - 256: 4.236 distance: 248 - 249: 9.847 distance: 248 - 257: 4.862 distance: 248 - 258: 3.007 distance: 249 - 250: 5.575 distance: 249 - 259: 6.532 distance: 249 - 260: 3.703 distance: 250 - 261: 3.248 distance: 250 - 262: 3.271 distance: 250 - 263: 4.896 distance: 264 - 272: 3.805 distance: 265 - 266: 11.141 distance: 265 - 268: 5.670 distance: 265 - 273: 4.716 distance: 266 - 267: 11.574 distance: 266 - 278: 13.262 distance: 268 - 269: 4.688 distance: 268 - 270: 4.070 distance: 269 - 271: 7.770 distance: 270 - 276: 4.897 distance: 270 - 277: 3.311 distance: 278 - 279: 4.841 distance: 278 - 286: 5.663 distance: 278 - 395: 6.409 distance: 279 - 280: 3.434 distance: 279 - 282: 6.642 distance: 279 - 287: 5.885 distance: 280 - 281: 15.948 distance: 280 - 297: 9.486 distance: 281 - 392: 20.284 distance: 282 - 283: 3.275 distance: 282 - 288: 4.847 distance: 282 - 289: 4.074 distance: 283 - 284: 3.107 distance: 283 - 290: 3.567 distance: 297 - 298: 4.761 distance: 297 - 305: 11.463 distance: 298 - 299: 19.233 distance: 298 - 301: 16.920 distance: 298 - 306: 14.270 distance: 299 - 300: 11.045 distance: 299 - 311: 15.055 distance: 301 - 302: 3.519 distance: 301 - 307: 10.993 distance: 301 - 308: 6.845 distance: 302 - 303: 8.625 distance: 302 - 304: 5.843 distance: 304 - 309: 4.875 distance: 304 - 310: 7.052 distance: 311 - 312: 8.306 distance: 311 - 318: 21.136 distance: 312 - 313: 4.075 distance: 312 - 315: 14.041 distance: 312 - 319: 6.804 distance: 313 - 314: 17.904 distance: 313 - 325: 10.472 distance: 315 - 316: 11.456 distance: 315 - 317: 5.430 distance: 315 - 320: 12.530 distance: 316 - 321: 19.237 distance: 317 - 323: 4.875 distance: 325 - 326: 6.717 distance: 325 - 331: 5.588 distance: 326 - 327: 5.435 distance: 326 - 332: 3.434 distance: 327 - 328: 29.264 distance: 327 - 339: 7.895 distance: 329 - 333: 5.607 distance: 330 - 335: 3.102 distance: 330 - 336: 3.356 distance: 331 - 337: 4.429 distance: 331 - 338: 3.161 distance: 339 - 340: 3.424 distance: 339 - 347: 13.634 distance: 340 - 341: 8.190 distance: 340 - 343: 4.192 distance: 340 - 348: 4.754 distance: 341 - 342: 27.957 distance: 341 - 353: 27.565 distance: 343 - 344: 4.166 distance: 343 - 349: 4.909 distance: 343 - 350: 7.347 distance: 344 - 346: 5.042 distance: 353 - 354: 16.903 distance: 353 - 359: 14.123 distance: 354 - 355: 4.582 distance: 354 - 357: 12.297 distance: 354 - 360: 18.318 distance: 355 - 356: 7.907 distance: 355 - 363: 5.474 distance: 357 - 358: 9.545 distance: 357 - 361: 9.925 distance: 357 - 362: 6.449 distance: 363 - 364: 4.894 distance: 363 - 368: 19.755 distance: 364 - 365: 8.758 distance: 364 - 367: 10.506 distance: 364 - 369: 12.663 distance: 365 - 366: 15.763 distance: 365 - 373: 7.205 distance: 367 - 370: 4.143 distance: 367 - 372: 4.265