Starting phenix.real_space_refine on Thu Jan 18 07:27:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg2_31963/01_2024/7vg2_31963.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg2_31963/01_2024/7vg2_31963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg2_31963/01_2024/7vg2_31963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg2_31963/01_2024/7vg2_31963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg2_31963/01_2024/7vg2_31963.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg2_31963/01_2024/7vg2_31963.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 P 71 5.49 5 S 35 5.16 5 C 4939 2.51 5 N 1402 2.21 5 O 1753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 627": "NH1" <-> "NH2" Residue "A PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "A ARG 931": "NH1" <-> "NH2" Residue "A ARG 933": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A ARG 968": "NH1" <-> "NH2" Residue "A PHE 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1013": "NH1" <-> "NH2" Residue "A ASP 1019": "OD1" <-> "OD2" Residue "A ARG 1057": "NH1" <-> "NH2" Residue "A ARG 1076": "NH1" <-> "NH2" Residue "A PHE 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1222": "NH1" <-> "NH2" Residue "A GLU 1224": "OE1" <-> "OE2" Residue "A PHE 1340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1373": "NH1" <-> "NH2" Residue "A ARG 1423": "NH1" <-> "NH2" Residue "A ARG 1478": "NH1" <-> "NH2" Residue "A ASP 1544": "OD1" <-> "OD2" 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: 8203 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6695 Classifications: {'peptide': 845} Link IDs: {'PTRANS': 38, 'TRANS': 806} Chain breaks: 7 Chain: "C" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 743 Classifications: {'RNA': 35} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 16} Link IDs: {'rna2p': 2, 'rna3p': 32} Chain: "D" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 762 Classifications: {'RNA': 36} Modifications used: {'rna3p_pur': 17, 'rna3p_pyr': 19} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3250 SG CYS A1091 80.111 40.909 60.628 1.00 37.81 S ATOM 3265 SG CYS A1093 77.913 44.550 59.990 1.00 40.00 S ATOM 3469 SG CYS A1119 77.965 41.631 57.831 1.00 29.71 S Time building chain proxies: 5.60, per 1000 atoms: 0.68 Number of scatterers: 8203 At special positions: 0 Unit cell: (116.6, 107.8, 97.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Ca 2 19.99 S 35 16.00 P 71 15.00 O 1753 8.00 N 1402 7.00 C 4939 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: 4.07 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" ND1 HIS A1123 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1119 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1093 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1091 " Number of angles added : 3 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1604 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 6 sheets defined 43.4% alpha, 9.7% beta 29 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 710 through 729 Processing helix chain 'A' and resid 778 through 795 removed outlier: 3.711A pdb=" N ILE A 782 " --> pdb=" O ASP A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 888 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 952 through 960 removed outlier: 3.812A pdb=" N TYR A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 983 Processing helix chain 'A' and resid 992 through 1000 Processing helix chain 'A' and resid 1011 through 1034 Processing helix chain 'A' and resid 1038 through 1050 Processing helix chain 'A' and resid 1051 through 1061 Processing helix chain 'A' and resid 1128 through 1159 removed outlier: 3.836A pdb=" N SER A1132 " --> pdb=" O SER A1128 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU A1148 " --> pdb=" O VAL A1144 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N SER A1149 " --> pdb=" O SER A1145 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A1150 " --> pdb=" O GLY A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1174 removed outlier: 3.891A pdb=" N VAL A1169 " --> pdb=" O ASP A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1196 removed outlier: 3.643A pdb=" N GLU A1190 " --> pdb=" O ASP A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1210 Processing helix chain 'A' and resid 1211 through 1215 Processing helix chain 'A' and resid 1220 through 1243 removed outlier: 3.627A pdb=" N SER A1229 " --> pdb=" O PHE A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1259 removed outlier: 3.647A pdb=" N ALA A1257 " --> pdb=" O ASP A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1271 Processing helix chain 'A' and resid 1272 through 1276 removed outlier: 4.069A pdb=" N THR A1275 " --> pdb=" O ASN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1294 Processing helix chain 'A' and resid 1311 through 1329 removed outlier: 4.232A pdb=" N GLY A1315 " --> pdb=" O PRO A1311 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A1318 " --> pdb=" O LEU A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1341 Processing helix chain 'A' and resid 1356 through 1369 Processing helix chain 'A' and resid 1405 through 1422 Processing helix chain 'A' and resid 1475 through 1488 Processing helix chain 'A' and resid 1544 through 1563 removed outlier: 3.680A pdb=" N SER A1548 " --> pdb=" O ASP A1544 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A1549 " --> pdb=" O LYS A1545 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1107 through 1108 Processing sheet with id=AA2, first strand: chain 'A' and resid 687 through 691 removed outlier: 5.545A pdb=" N ALA A 654 " --> pdb=" O CYS A 704 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLN A 706 " --> pdb=" O PHE A 652 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE A 652 " --> pdb=" O GLN A 706 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 828 through 829 Processing sheet with id=AA4, first strand: chain 'A' and resid 938 through 941 removed outlier: 6.427A pdb=" N LYS A 903 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE A 856 " --> pdb=" O LYS A 903 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1372 through 1377 Processing sheet with id=AA6, first strand: chain 'A' and resid 1494 through 1496 removed outlier: 3.636A pdb=" N VAL A1535 " --> pdb=" O LEU A1527 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 885 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1631 1.32 - 1.45: 2389 1.45 - 1.57: 4301 1.57 - 1.69: 139 1.69 - 1.81: 52 Bond restraints: 8512 Sorted by residual: bond pdb=" P A C 1 " pdb=" OP3 A C 1 " ideal model delta sigma weight residual 1.480 1.600 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CB THR A1236 " pdb=" CG2 THR A1236 " ideal model delta sigma weight residual 1.521 1.380 0.141 3.30e-02 9.18e+02 1.82e+01 bond pdb=" SD MET A1011 " pdb=" CE MET A1011 " ideal model delta sigma weight residual 1.791 1.701 0.090 2.50e-02 1.60e+03 1.29e+01 bond pdb=" CB ARG A1062 " pdb=" CG ARG A1062 " ideal model delta sigma weight residual 1.520 1.413 0.107 3.00e-02 1.11e+03 1.27e+01 bond pdb=" CB ASN A 726 " pdb=" CG ASN A 726 " ideal model delta sigma weight residual 1.516 1.429 0.087 2.50e-02 1.60e+03 1.22e+01 ... (remaining 8507 not shown) Histogram of bond angle deviations from ideal: 93.52 - 101.70: 122 101.70 - 109.88: 2220 109.88 - 118.06: 4681 118.06 - 126.24: 4503 126.24 - 134.42: 319 Bond angle restraints: 11845 Sorted by residual: angle pdb=" CA ASN A1405 " pdb=" CB ASN A1405 " pdb=" CG ASN A1405 " ideal model delta sigma weight residual 112.60 117.81 -5.21 1.00e+00 1.00e+00 2.71e+01 angle pdb=" N PRO A1006 " pdb=" CA PRO A1006 " pdb=" C PRO A1006 " ideal model delta sigma weight residual 110.95 103.02 7.93 1.62e+00 3.81e-01 2.40e+01 angle pdb=" C THR A1404 " pdb=" N ASN A1405 " pdb=" CA ASN A1405 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" N GLY A 649 " pdb=" CA GLY A 649 " pdb=" C GLY A 649 " ideal model delta sigma weight residual 111.36 116.80 -5.44 1.17e+00 7.31e-01 2.16e+01 angle pdb=" C LEU A 763 " pdb=" CA LEU A 763 " pdb=" CB LEU A 763 " ideal model delta sigma weight residual 109.75 117.22 -7.47 1.65e+00 3.67e-01 2.05e+01 ... (remaining 11840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 4548 15.87 - 31.74: 371 31.74 - 47.61: 116 47.61 - 63.47: 66 63.47 - 79.34: 36 Dihedral angle restraints: 5137 sinusoidal: 2672 harmonic: 2465 Sorted by residual: dihedral pdb=" CA PHE A1164 " pdb=" C PHE A1164 " pdb=" N ASP A1165 " pdb=" CA ASP A1165 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA ASP A1165 " pdb=" C ASP A1165 " pdb=" N PRO A1166 " pdb=" CA PRO A1166 " ideal model delta harmonic sigma weight residual -180.00 -150.82 -29.18 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA GLY A1310 " pdb=" C GLY A1310 " pdb=" N PRO A1311 " pdb=" CA PRO A1311 " ideal model delta harmonic sigma weight residual -180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 5134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1097 0.096 - 0.191: 260 0.191 - 0.287: 30 0.287 - 0.382: 7 0.382 - 0.478: 5 Chirality restraints: 1399 Sorted by residual: chirality pdb=" CG LEU A1556 " pdb=" CB LEU A1556 " pdb=" CD1 LEU A1556 " pdb=" CD2 LEU A1556 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" CB VAL A1374 " pdb=" CA VAL A1374 " pdb=" CG1 VAL A1374 " pdb=" CG2 VAL A1374 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CA LEU A 763 " pdb=" N LEU A 763 " pdb=" C LEU A 763 " pdb=" CB LEU A 763 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 1396 not shown) Planarity restraints: 1251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1142 " -0.042 2.00e-02 2.50e+03 3.37e-02 2.27e+01 pdb=" CG TYR A1142 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A1142 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A1142 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A1142 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A1142 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A1142 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR A1142 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 19 " -0.047 2.00e-02 2.50e+03 3.03e-02 2.07e+01 pdb=" N1 U C 19 " 0.075 2.00e-02 2.50e+03 pdb=" C2 U C 19 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U C 19 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U C 19 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U C 19 " -0.021 2.00e-02 2.50e+03 pdb=" O4 U C 19 " -0.000 2.00e-02 2.50e+03 pdb=" C5 U C 19 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U C 19 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1243 " -0.043 2.00e-02 2.50e+03 3.02e-02 1.82e+01 pdb=" CG TYR A1243 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR A1243 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A1243 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A1243 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A1243 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A1243 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR A1243 " -0.005 2.00e-02 2.50e+03 ... (remaining 1248 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 38 2.44 - 3.05: 5021 3.05 - 3.67: 14133 3.67 - 4.28: 21155 4.28 - 4.90: 32202 Nonbonded interactions: 72549 Sorted by model distance: nonbonded pdb=" OD1 ASP A1316 " pdb="CA CA A2002 " model vdw 1.822 2.510 nonbonded pdb=" OE1 GLU A1136 " pdb="CA CA A2001 " model vdw 2.072 2.510 nonbonded pdb=" OE1 GLU A1224 " pdb=" OD1 ASP A1316 " model vdw 2.201 3.040 nonbonded pdb=" OD1 ASP A1228 " pdb=" OE2 GLU A1319 " model vdw 2.208 3.040 nonbonded pdb=" OP1 U C 25 " pdb="CA CA A2002 " model vdw 2.208 2.510 ... (remaining 72544 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.000 Extract box with map and model: 3.280 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 31.350 Find NCS groups from input model: 0.190 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 : 0.016 0.141 8512 Z= 1.044 Angle : 1.432 10.314 11845 Z= 0.815 Chirality : 0.086 0.478 1399 Planarity : 0.010 0.075 1251 Dihedral : 15.756 79.342 3533 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.96 % Favored : 91.80 % Rotamer: Outliers : 1.74 % Allowed : 7.61 % Favored : 90.65 % Cbeta Deviations : 0.12 % 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: -3.84 (0.23), residues: 829 helix: -2.53 (0.20), residues: 344 sheet: -2.14 (0.42), residues: 127 loop : -2.57 (0.27), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.007 TRP A1078 HIS 0.016 0.005 HIS A1153 PHE 0.044 0.007 PHE A 745 TYR 0.076 0.008 TYR A1142 ARG 0.031 0.003 ARG A 968 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 694 ARG cc_start: 0.6876 (mmp80) cc_final: 0.6627 (mmp80) REVERT: A 734 VAL cc_start: 0.8509 (p) cc_final: 0.7764 (m) REVERT: A 841 GLU cc_start: 0.6559 (pp20) cc_final: 0.6295 (pp20) REVERT: A 860 VAL cc_start: 0.6086 (t) cc_final: 0.5857 (m) REVERT: A 1145 SER cc_start: 0.8398 (m) cc_final: 0.8136 (m) REVERT: A 1283 VAL cc_start: 0.8676 (p) cc_final: 0.8466 (m) REVERT: A 1472 MET cc_start: 0.5510 (mmt) cc_final: 0.5079 (mmt) outliers start: 13 outliers final: 5 residues processed: 142 average time/residue: 0.2388 time to fit residues: 44.6481 Evaluate side-chains 102 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1232 ASP Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1524 THR Chi-restraints excluded: chain A residue 1537 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 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 653 GLN A1045 GLN A1241 ASN ** A1278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 ASN A1488 HIS A1569 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8512 Z= 0.223 Angle : 0.664 8.767 11845 Z= 0.343 Chirality : 0.040 0.192 1399 Planarity : 0.005 0.051 1251 Dihedral : 15.723 74.016 1902 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.21 % Rotamer: Outliers : 3.74 % Allowed : 9.48 % Favored : 86.78 % 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: -2.09 (0.26), residues: 829 helix: -0.66 (0.24), residues: 353 sheet: -1.91 (0.44), residues: 129 loop : -1.83 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 779 HIS 0.005 0.001 HIS A1276 PHE 0.015 0.002 PHE A 724 TYR 0.019 0.002 TYR A1142 ARG 0.005 0.000 ARG A1515 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 0.839 Fit side-chains REVERT: A 734 VAL cc_start: 0.8266 (p) cc_final: 0.7594 (m) REVERT: A 841 GLU cc_start: 0.6513 (pp20) cc_final: 0.6083 (pp20) REVERT: A 1019 ASP cc_start: 0.6953 (t0) cc_final: 0.6439 (t70) REVERT: A 1038 ASP cc_start: 0.7863 (p0) cc_final: 0.7591 (p0) REVERT: A 1085 SER cc_start: 0.8707 (m) cc_final: 0.8426 (p) REVERT: A 1145 SER cc_start: 0.7992 (m) cc_final: 0.7736 (m) REVERT: A 1406 LYS cc_start: 0.8098 (tppp) cc_final: 0.7815 (ttmt) REVERT: A 1528 ARG cc_start: 0.7437 (mpp80) cc_final: 0.6459 (mmm160) outliers start: 28 outliers final: 18 residues processed: 148 average time/residue: 0.2225 time to fit residues: 44.5956 Evaluate side-chains 124 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain A residue 1232 ASP Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1399 ASP Chi-restraints excluded: chain A residue 1516 THR Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1524 THR Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1537 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1196 GLN A1197 HIS A1261 ASN ** A1278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8512 Z= 0.264 Angle : 0.647 9.649 11845 Z= 0.330 Chirality : 0.040 0.290 1399 Planarity : 0.005 0.056 1251 Dihedral : 15.459 73.964 1900 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.24 % Favored : 92.64 % Rotamer: Outliers : 5.07 % Allowed : 12.28 % Favored : 82.64 % 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: -1.21 (0.28), residues: 829 helix: 0.28 (0.26), residues: 356 sheet: -1.70 (0.46), residues: 130 loop : -1.50 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1125 HIS 0.005 0.001 HIS A1276 PHE 0.017 0.002 PHE A1203 TYR 0.017 0.002 TYR A1142 ARG 0.004 0.000 ARG A1515 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 109 time to evaluate : 0.895 Fit side-chains REVERT: A 734 VAL cc_start: 0.8369 (p) cc_final: 0.7787 (m) REVERT: A 841 GLU cc_start: 0.6556 (pp20) cc_final: 0.6189 (pp20) REVERT: A 1019 ASP cc_start: 0.6933 (t0) cc_final: 0.6503 (t70) REVERT: A 1038 ASP cc_start: 0.7783 (p0) cc_final: 0.7527 (p0) REVERT: A 1085 SER cc_start: 0.8733 (m) cc_final: 0.8399 (p) REVERT: A 1224 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6844 (tt0) REVERT: A 1417 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6782 (mp) REVERT: A 1528 ARG cc_start: 0.7430 (mpp80) cc_final: 0.6380 (mmm160) outliers start: 38 outliers final: 27 residues processed: 138 average time/residue: 0.2287 time to fit residues: 42.2558 Evaluate side-chains 129 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain A residue 1224 GLU Chi-restraints excluded: chain A residue 1232 ASP Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1399 ASP Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1516 THR Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1566 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 967 HIS ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8512 Z= 0.229 Angle : 0.617 9.708 11845 Z= 0.313 Chirality : 0.039 0.223 1399 Planarity : 0.004 0.054 1251 Dihedral : 15.295 74.021 1897 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.39 % Favored : 93.49 % Rotamer: Outliers : 5.61 % Allowed : 14.69 % Favored : 79.71 % 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: -0.73 (0.29), residues: 829 helix: 0.72 (0.26), residues: 361 sheet: -1.58 (0.46), residues: 128 loop : -1.28 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1125 HIS 0.005 0.001 HIS A1276 PHE 0.015 0.002 PHE A1203 TYR 0.016 0.002 TYR A1220 ARG 0.004 0.000 ARG A1515 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 111 time to evaluate : 0.829 Fit side-chains REVERT: A 734 VAL cc_start: 0.8365 (p) cc_final: 0.7815 (m) REVERT: A 841 GLU cc_start: 0.6553 (pp20) cc_final: 0.6314 (pp20) REVERT: A 1019 ASP cc_start: 0.7012 (t70) cc_final: 0.6562 (t70) REVERT: A 1085 SER cc_start: 0.8702 (m) cc_final: 0.8380 (p) REVERT: A 1164 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.5481 (t80) REVERT: A 1417 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6629 (mp) REVERT: A 1499 GLU cc_start: 0.5901 (tt0) cc_final: 0.5483 (pm20) REVERT: A 1528 ARG cc_start: 0.7261 (mpp80) cc_final: 0.6231 (mmm160) outliers start: 42 outliers final: 32 residues processed: 139 average time/residue: 0.2285 time to fit residues: 42.3540 Evaluate side-chains 135 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 101 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1232 ASP Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1399 ASP Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1516 THR Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1523 SER Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1537 TYR Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1566 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 71.047 > 50: distance: 4 - 9: 34.194 distance: 9 - 10: 33.196 distance: 10 - 11: 40.379 distance: 10 - 13: 40.636 distance: 11 - 12: 40.507 distance: 11 - 15: 39.372 distance: 13 - 14: 57.001 distance: 15 - 16: 40.073 distance: 16 - 17: 40.770 distance: 16 - 19: 55.970 distance: 17 - 18: 54.396 distance: 17 - 24: 38.041 distance: 19 - 20: 41.075 distance: 20 - 21: 28.202 distance: 21 - 22: 50.323 distance: 21 - 23: 31.533 distance: 25 - 26: 41.602 distance: 25 - 28: 41.608 distance: 26 - 27: 20.804 distance: 26 - 33: 31.594 distance: 28 - 29: 38.680 distance: 29 - 30: 37.171 distance: 30 - 31: 26.115 distance: 30 - 32: 36.040 distance: 33 - 34: 16.948 distance: 34 - 35: 36.773 distance: 35 - 36: 40.690 distance: 35 - 42: 53.090 distance: 37 - 38: 45.913 distance: 38 - 39: 38.754 distance: 39 - 40: 11.051 distance: 40 - 41: 43.187 distance: 43 - 44: 40.078 distance: 43 - 46: 57.455 distance: 44 - 45: 47.146 distance: 44 - 48: 58.180 distance: 46 - 47: 43.331 distance: 48 - 49: 28.687 distance: 49 - 52: 57.570 distance: 50 - 51: 56.025 distance: 50 - 59: 39.437 distance: 52 - 53: 43.640 distance: 53 - 54: 19.056 distance: 54 - 55: 66.762 distance: 55 - 56: 30.851 distance: 56 - 57: 6.524 distance: 56 - 58: 22.403 distance: 60 - 63: 40.854 distance: 61 - 62: 56.085 distance: 61 - 66: 43.523 distance: 63 - 64: 49.373 distance: 63 - 65: 30.192 distance: 66 - 67: 14.562 distance: 66 - 72: 46.800 distance: 67 - 68: 47.270 distance: 67 - 70: 41.449 distance: 68 - 69: 4.955 distance: 68 - 73: 30.615 distance: 70 - 71: 55.911 distance: 71 - 72: 54.320 distance: 73 - 74: 20.209 distance: 74 - 75: 16.751 distance: 74 - 77: 18.213 distance: 75 - 76: 38.992 distance: 77 - 78: 20.888 distance: 78 - 79: 9.198 distance: 78 - 80: 7.610 distance: 79 - 81: 8.845 distance: 80 - 82: 13.643 distance: 81 - 83: 5.214 distance: 82 - 83: 5.827 distance: 84 - 85: 4.192 distance: 85 - 86: 16.174 distance: 85 - 88: 12.681 distance: 86 - 87: 34.355 distance: 86 - 93: 13.672 distance: 88 - 89: 7.226 distance: 89 - 90: 8.971 distance: 90 - 91: 6.869 distance: 90 - 92: 7.153