Starting phenix.real_space_refine on Wed Jan 17 17:13:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pog_17791/01_2024/8pog_17791.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pog_17791/01_2024/8pog_17791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pog_17791/01_2024/8pog_17791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pog_17791/01_2024/8pog_17791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pog_17791/01_2024/8pog_17791.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pog_17791/01_2024/8pog_17791.pdb" } resolution = 4.15 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= 0.024 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 24 5.16 5 C 3132 2.51 5 N 880 2.21 5 O 928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 6": "OE1" <-> "OE2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C ASP 108": "OD1" <-> "OD2" Residue "D PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 4964 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1241 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "B" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1241 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "C" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1241 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "D" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1241 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Time building chain proxies: 3.24, per 1000 atoms: 0.65 Number of scatterers: 4964 At special positions: 0 Unit cell: (75.33, 87.42, 79.05, 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 24 16.00 O 928 8.00 N 880 7.00 C 3132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 888.7 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1144 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 59.0% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 removed outlier: 3.547A pdb=" N LEU A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 39 Processing helix chain 'A' and resid 43 through 58 removed outlier: 3.630A pdb=" N TYR A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 81 Processing helix chain 'A' and resid 106 through 130 removed outlier: 3.503A pdb=" N GLN A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'B' and resid 7 through 19 removed outlier: 3.705A pdb=" N LEU B 11 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 39 Processing helix chain 'B' and resid 43 through 58 removed outlier: 3.528A pdb=" N GLN B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 81 Processing helix chain 'B' and resid 106 through 130 removed outlier: 4.524A pdb=" N SER B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ARG B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'C' and resid 7 through 19 removed outlier: 3.682A pdb=" N LEU C 11 " --> pdb=" O ASN C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 39 Processing helix chain 'C' and resid 43 through 58 removed outlier: 3.511A pdb=" N LEU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 81 Processing helix chain 'C' and resid 106 through 130 removed outlier: 4.609A pdb=" N SER C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ARG C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'D' and resid 7 through 19 removed outlier: 3.627A pdb=" N LEU D 11 " --> pdb=" O ASN D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 39 Processing helix chain 'D' and resid 43 through 58 removed outlier: 3.621A pdb=" N GLN D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 81 Processing helix chain 'D' and resid 106 through 130 removed outlier: 4.572A pdb=" N SER D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARG D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 133 No H-bonds generated for 'chain 'D' and resid 131 through 133' Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89 removed outlier: 3.571A pdb=" N CYS A 84 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASP A 150 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU A 145 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLN A 152 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU A 143 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 141 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 84 through 89 removed outlier: 3.525A pdb=" N CYS B 84 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ASP B 150 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU B 145 " --> pdb=" O ASP B 150 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N GLN B 152 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU B 143 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 141 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS B 156 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR B 139 " --> pdb=" O HIS B 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 89 removed outlier: 3.556A pdb=" N CYS C 84 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASP C 150 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU C 145 " --> pdb=" O ASP C 150 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLN C 152 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU C 143 " --> pdb=" O GLN C 152 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS C 156 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR C 139 " --> pdb=" O HIS C 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 84 through 89 removed outlier: 3.518A pdb=" N CYS D 84 " --> pdb=" O GLN D 99 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASP D 150 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU D 145 " --> pdb=" O ASP D 150 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLN D 152 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU D 143 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 154 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 141 " --> pdb=" O ARG D 154 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 885 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: 1.26 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1696 1.34 - 1.46: 1031 1.46 - 1.58: 2317 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 5080 Sorted by residual: bond pdb=" CB GLN A 132 " pdb=" CG GLN A 132 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" C VAL B 38 " pdb=" O VAL B 38 " ideal model delta sigma weight residual 1.231 1.241 -0.010 1.02e-02 9.61e+03 9.70e-01 bond pdb=" CB GLU C 40 " pdb=" CG GLU C 40 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.84e-01 bond pdb=" C VAL D 38 " pdb=" O VAL D 38 " ideal model delta sigma weight residual 1.231 1.241 -0.010 1.07e-02 8.73e+03 8.43e-01 bond pdb=" C VAL A 38 " pdb=" O VAL A 38 " ideal model delta sigma weight residual 1.231 1.240 -0.009 1.07e-02 8.73e+03 7.60e-01 ... (remaining 5075 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.08: 144 107.08 - 113.82: 2752 113.82 - 120.55: 2084 120.55 - 127.29: 1844 127.29 - 134.03: 80 Bond angle restraints: 6904 Sorted by residual: angle pdb=" CA GLU C 40 " pdb=" CB GLU C 40 " pdb=" CG GLU C 40 " ideal model delta sigma weight residual 114.10 119.39 -5.29 2.00e+00 2.50e-01 7.01e+00 angle pdb=" CB GLN A 132 " pdb=" CG GLN A 132 " pdb=" CD GLN A 132 " ideal model delta sigma weight residual 112.60 116.58 -3.98 1.70e+00 3.46e-01 5.48e+00 angle pdb=" CA GLN A 132 " pdb=" CB GLN A 132 " pdb=" CG GLN A 132 " ideal model delta sigma weight residual 114.10 118.40 -4.30 2.00e+00 2.50e-01 4.61e+00 angle pdb=" N VAL B 38 " pdb=" CA VAL B 38 " pdb=" C VAL B 38 " ideal model delta sigma weight residual 111.81 113.58 -1.77 8.60e-01 1.35e+00 4.24e+00 angle pdb=" CA GLU B 40 " pdb=" CB GLU B 40 " pdb=" CG GLU B 40 " ideal model delta sigma weight residual 114.10 118.17 -4.07 2.00e+00 2.50e-01 4.14e+00 ... (remaining 6899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2639 17.95 - 35.89: 254 35.89 - 53.84: 56 53.84 - 71.79: 13 71.79 - 89.73: 10 Dihedral angle restraints: 2972 sinusoidal: 1196 harmonic: 1776 Sorted by residual: dihedral pdb=" CB GLU D 86 " pdb=" CG GLU D 86 " pdb=" CD GLU D 86 " pdb=" OE1 GLU D 86 " ideal model delta sinusoidal sigma weight residual 0.00 89.73 -89.73 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU C 86 " pdb=" CG GLU C 86 " pdb=" CD GLU C 86 " pdb=" OE1 GLU C 86 " ideal model delta sinusoidal sigma weight residual 0.00 89.73 -89.73 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 86 " pdb=" CG GLU B 86 " pdb=" CD GLU B 86 " pdb=" OE1 GLU B 86 " ideal model delta sinusoidal sigma weight residual 0.00 89.63 -89.63 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 2969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 476 0.026 - 0.051: 173 0.051 - 0.077: 47 0.077 - 0.102: 39 0.102 - 0.128: 13 Chirality restraints: 748 Sorted by residual: chirality pdb=" CA VAL B 151 " pdb=" N VAL B 151 " pdb=" C VAL B 151 " pdb=" CB VAL B 151 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA VAL B 140 " pdb=" N VAL B 140 " pdb=" C VAL B 140 " pdb=" CB VAL B 140 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA VAL D 151 " pdb=" N VAL D 151 " pdb=" C VAL D 151 " pdb=" CB VAL D 151 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.37e-01 ... (remaining 745 not shown) Planarity restraints: 908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 124 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C LEU B 124 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU B 124 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR B 125 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 124 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C LEU A 124 " -0.032 2.00e-02 2.50e+03 pdb=" O LEU A 124 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR A 125 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 122 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" C GLU B 122 " -0.030 2.00e-02 2.50e+03 pdb=" O GLU B 122 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY B 123 " 0.010 2.00e-02 2.50e+03 ... (remaining 905 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 979 2.77 - 3.31: 4882 3.31 - 3.84: 7703 3.84 - 4.37: 8138 4.37 - 4.90: 14428 Nonbonded interactions: 36130 Sorted by model distance: nonbonded pdb=" OG SER B 90 " pdb=" OD1 ASP B 93 " model vdw 2.242 2.440 nonbonded pdb=" OD1 ASP D 56 " pdb=" NH1 ARG D 127 " model vdw 2.258 2.520 nonbonded pdb=" OD2 ASP B 93 " pdb=" NH1 ARG B 154 " model vdw 2.258 2.520 nonbonded pdb=" N GLU A 42 " pdb=" OE1 GLU A 42 " model vdw 2.286 2.520 nonbonded pdb=" OD1 ASP C 56 " pdb=" NH1 ARG C 127 " model vdw 2.307 2.520 ... (remaining 36125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 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: 1.190 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: 4.770 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.590 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 0.033 5080 Z= 0.171 Angle : 0.588 5.841 6904 Z= 0.333 Chirality : 0.037 0.128 748 Planarity : 0.005 0.039 908 Dihedral : 15.834 89.734 1828 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 0.40 (0.33), residues: 616 helix: 0.73 (0.28), residues: 336 sheet: 0.14 (0.55), residues: 84 loop : -0.26 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 13 HIS 0.002 0.000 HIS B 98 PHE 0.008 0.001 PHE C 46 TYR 0.014 0.001 TYR C 58 ARG 0.009 0.001 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: B 40 GLU cc_start: 0.5649 (pm20) cc_final: 0.5189 (tt0) REVERT: B 64 GLU cc_start: 0.5687 (mm-30) cc_final: 0.5463 (mp0) REVERT: B 72 ASN cc_start: 0.7195 (m110) cc_final: 0.6715 (m110) REVERT: B 148 LEU cc_start: 0.8423 (mt) cc_final: 0.8159 (mt) REVERT: C 72 ASN cc_start: 0.6919 (m110) cc_final: 0.6543 (m110) REVERT: C 142 ARG cc_start: 0.8322 (mtp-110) cc_final: 0.7978 (mtm110) REVERT: C 148 LEU cc_start: 0.8582 (mt) cc_final: 0.8217 (mt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1492 time to fit residues: 23.5334 Evaluate side-chains 107 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.0980 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 0.0970 chunk 54 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5080 Z= 0.217 Angle : 0.497 4.573 6904 Z= 0.265 Chirality : 0.038 0.121 748 Planarity : 0.004 0.022 908 Dihedral : 3.566 13.915 676 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.34), residues: 616 helix: 2.49 (0.27), residues: 340 sheet: 0.11 (0.55), residues: 84 loop : -0.45 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 128 HIS 0.004 0.001 HIS A 98 PHE 0.010 0.002 PHE C 80 TYR 0.004 0.001 TYR B 58 ARG 0.006 0.001 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7395 (tp30) cc_final: 0.6738 (tp30) REVERT: A 72 ASN cc_start: 0.7033 (m110) cc_final: 0.6654 (m110) REVERT: B 72 ASN cc_start: 0.7166 (m110) cc_final: 0.6948 (m110) REVERT: B 141 SER cc_start: 0.8498 (t) cc_final: 0.8272 (t) REVERT: C 17 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8110 (tp40) REVERT: C 96 LEU cc_start: 0.9054 (mm) cc_final: 0.8794 (mp) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1444 time to fit residues: 22.7861 Evaluate side-chains 109 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 chunk 18 optimal weight: 0.4980 chunk 43 optimal weight: 0.0040 chunk 53 optimal weight: 0.7980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5080 Z= 0.152 Angle : 0.463 4.902 6904 Z= 0.234 Chirality : 0.037 0.123 748 Planarity : 0.003 0.023 908 Dihedral : 3.355 13.337 676 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 2.44 (0.35), residues: 616 helix: 3.10 (0.28), residues: 340 sheet: 0.16 (0.54), residues: 84 loop : -0.50 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 113 HIS 0.003 0.001 HIS C 98 PHE 0.013 0.001 PHE B 153 TYR 0.006 0.001 TYR D 58 ARG 0.005 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7458 (tp30) cc_final: 0.6762 (tp30) REVERT: B 69 LEU cc_start: 0.8455 (tp) cc_final: 0.8035 (tp) REVERT: B 72 ASN cc_start: 0.7097 (m110) cc_final: 0.6836 (m110) REVERT: B 141 SER cc_start: 0.8535 (t) cc_final: 0.8282 (t) REVERT: B 153 PHE cc_start: 0.7891 (m-80) cc_final: 0.7688 (m-80) REVERT: C 17 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8063 (tp40) REVERT: D 148 LEU cc_start: 0.8260 (mt) cc_final: 0.8001 (mt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1389 time to fit residues: 21.3843 Evaluate side-chains 101 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 0.0470 chunk 32 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5080 Z= 0.193 Angle : 0.468 4.983 6904 Z= 0.239 Chirality : 0.037 0.115 748 Planarity : 0.003 0.024 908 Dihedral : 3.266 12.584 676 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 2.27 (0.35), residues: 616 helix: 2.84 (0.28), residues: 348 sheet: 0.23 (0.53), residues: 84 loop : -0.53 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 113 HIS 0.004 0.001 HIS A 98 PHE 0.009 0.002 PHE D 117 TYR 0.005 0.001 TYR D 58 ARG 0.005 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: B 72 ASN cc_start: 0.7107 (m110) cc_final: 0.6905 (m110) REVERT: C 17 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8037 (tp40) REVERT: C 142 ARG cc_start: 0.8262 (mtp-110) cc_final: 0.7974 (mtp85) REVERT: D 148 LEU cc_start: 0.8184 (mt) cc_final: 0.7960 (mt) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1404 time to fit residues: 20.4610 Evaluate side-chains 97 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.0050 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN B 115 HIS ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5080 Z= 0.182 Angle : 0.467 4.975 6904 Z= 0.236 Chirality : 0.036 0.117 748 Planarity : 0.003 0.024 908 Dihedral : 3.253 12.367 676 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 2.30 (0.34), residues: 616 helix: 2.91 (0.27), residues: 344 sheet: 0.27 (0.53), residues: 84 loop : -0.58 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 113 HIS 0.004 0.001 HIS A 98 PHE 0.009 0.001 PHE D 117 TYR 0.006 0.001 TYR D 58 ARG 0.006 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: C 17 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8050 (tp40) REVERT: D 148 LEU cc_start: 0.8181 (mt) cc_final: 0.7979 (mt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1341 time to fit residues: 19.7336 Evaluate side-chains 96 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 70.6244 > 50: distance: 42 - 47: 23.933 distance: 47 - 48: 4.524 distance: 48 - 49: 18.475 distance: 48 - 51: 20.228 distance: 49 - 50: 15.311 distance: 50 - 155: 26.341 distance: 51 - 52: 16.173 distance: 53 - 54: 56.911 distance: 54 - 55: 38.814 distance: 54 - 57: 28.013 distance: 55 - 56: 8.940 distance: 55 - 64: 40.406 distance: 57 - 58: 12.062 distance: 59 - 60: 6.706 distance: 60 - 61: 36.278 distance: 61 - 62: 10.360 distance: 61 - 63: 17.936 distance: 65 - 68: 15.032 distance: 66 - 67: 38.977 distance: 66 - 73: 65.331 distance: 68 - 69: 50.832 distance: 69 - 70: 31.234 distance: 70 - 71: 17.007 distance: 70 - 72: 30.774 distance: 73 - 74: 41.172 distance: 74 - 75: 17.720 distance: 74 - 77: 44.829 distance: 75 - 76: 41.034 distance: 75 - 84: 7.741 distance: 77 - 78: 21.186 distance: 78 - 79: 28.905 distance: 79 - 80: 16.065 distance: 80 - 81: 16.846 distance: 81 - 82: 21.533 distance: 81 - 83: 17.428 distance: 84 - 85: 37.231 distance: 85 - 86: 22.640 distance: 85 - 88: 17.262 distance: 86 - 87: 9.853 distance: 86 - 92: 54.979 distance: 88 - 89: 27.070 distance: 89 - 91: 3.305 distance: 94 - 95: 39.439 distance: 94 - 103: 40.824 distance: 96 - 97: 14.620 distance: 97 - 98: 33.275 distance: 97 - 99: 12.656 distance: 98 - 100: 22.005 distance: 99 - 101: 16.434 distance: 100 - 102: 7.237 distance: 101 - 102: 28.807 distance: 103 - 104: 27.221 distance: 104 - 105: 42.807 distance: 104 - 107: 36.200 distance: 105 - 106: 39.647 distance: 105 - 109: 41.098 distance: 109 - 110: 21.334 distance: 110 - 111: 20.468 distance: 110 - 113: 44.209 distance: 111 - 112: 34.448 distance: 111 - 117: 17.976 distance: 114 - 115: 40.305 distance: 117 - 118: 47.071 distance: 118 - 119: 42.935 distance: 119 - 120: 20.892 distance: 119 - 123: 20.827 distance: 121 - 122: 40.907 distance: 124 - 125: 40.021 distance: 124 - 127: 6.195 distance: 125 - 126: 15.584 distance: 125 - 131: 25.580 distance: 128 - 129: 4.849