Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:04:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcc_9067/12_2022/6mcc_9067_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcc_9067/12_2022/6mcc_9067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcc_9067/12_2022/6mcc_9067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcc_9067/12_2022/6mcc_9067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcc_9067/12_2022/6mcc_9067_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcc_9067/12_2022/6mcc_9067_updated_updated.pdb" } resolution = 3.9 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= 0.005 sd= 0.088 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 ARG 340": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A ARG 655": "NH1" <-> "NH2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 919": "NH1" <-> "NH2" Residue "A PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1333": "NH1" <-> "NH2" Residue "A ARG 1335": "NH1" <-> "NH2" Residue "C ARG 25": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 14175 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2494 Unusual residues: {'GTP': 1} Classifications: {'RNA': 115, 'undetermined': 1} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 41} Link IDs: {'rna2p': 18, 'rna3p': 96, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain: "A" Number of atoms: 10715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1364, 10715 Classifications: {'peptide': 1364} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 35, 'TRANS': 1328} Unresolved non-hydrogen bonds: 441 Unresolved non-hydrogen angles: 507 Unresolved non-hydrogen dihedrals: 389 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 7, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 226 Chain: "C" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 966 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'GLU:plan': 17, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 89 Time building chain proxies: 8.64, per 1000 atoms: 0.61 Number of scatterers: 14175 At special positions: 0 Unit cell: (92, 121.9, 144.9, 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 26 16.00 P 118 15.00 O 3022 8.00 N 2458 7.00 C 8551 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.37 Conformation dependent library (CDL) restraints added in 2.1 seconds 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 7 sheets defined 39.4% alpha, 6.8% beta 27 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 5.50 Creating SS restraints... Processing helix chain 'A' and resid 61 through 85 Processing helix chain 'A' and resid 90 through 93 No H-bonds generated for 'chain 'A' and resid 90 through 93' Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 123 through 131 Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.583A pdb=" N HIS A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 Processing helix chain 'A' and resid 208 through 211 No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 218 through 228 removed outlier: 5.250A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 246 Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.806A pdb=" N ASN A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 305 removed outlier: 5.711A pdb=" N ASP A 288 " --> pdb=" O GLN A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 339 removed outlier: 3.553A pdb=" N ILE A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.689A pdb=" N ILE A 363 " --> pdb=" O TYR A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 359 through 363' Processing helix chain 'A' and resid 369 through 382 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 390 through 393 No H-bonds generated for 'chain 'A' and resid 390 through 393' Processing helix chain 'A' and resid 412 through 424 Processing helix chain 'A' and resid 432 through 435 removed outlier: 3.771A pdb=" N ASP A 435 " --> pdb=" O PHE A 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 435' Processing helix chain 'A' and resid 437 through 445 Processing helix chain 'A' and resid 475 through 477 No H-bonds generated for 'chain 'A' and resid 475 through 477' Processing helix chain 'A' and resid 485 through 494 removed outlier: 3.670A pdb=" N GLU A 493 " --> pdb=" O GLN A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 605 through 608 No H-bonds generated for 'chain 'A' and resid 605 through 608' Processing helix chain 'A' and resid 613 through 625 Processing helix chain 'A' and resid 631 through 639 removed outlier: 4.182A pdb=" N ARG A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 638 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 651 No H-bonds generated for 'chain 'A' and resid 648 through 651' Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'A' and resid 703 through 711 removed outlier: 4.003A pdb=" N ALA A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 726 removed outlier: 4.293A pdb=" N ASN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 750 removed outlier: 4.280A pdb=" N LYS A 749 " --> pdb=" O ASP A 745 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 772 No H-bonds generated for 'chain 'A' and resid 770 through 772' Processing helix chain 'A' and resid 775 through 778 No H-bonds generated for 'chain 'A' and resid 775 through 778' Processing helix chain 'A' and resid 781 through 790 removed outlier: 3.844A pdb=" N ILE A 788 " --> pdb=" O GLU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 809 through 817 removed outlier: 3.570A pdb=" N GLN A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 863 No H-bonds generated for 'chain 'A' and resid 861 through 863' Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 880 through 888 removed outlier: 3.727A pdb=" N ARG A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 885 " --> pdb=" O ASN A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 903 removed outlier: 3.908A pdb=" N LYS A 902 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ALA A 903 " --> pdb=" O ASN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 919 Processing helix chain 'A' and resid 926 through 939 removed outlier: 3.989A pdb=" N MET A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 968 Processing helix chain 'A' and resid 981 through 998 removed outlier: 3.894A pdb=" N ASP A 986 " --> pdb=" O HIS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1005 No H-bonds generated for 'chain 'A' and resid 1003 through 1005' Processing helix chain 'A' and resid 1042 through 1045 Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1080 through 1087 Processing helix chain 'A' and resid 1171 through 1176 Processing helix chain 'A' and resid 1178 through 1185 Processing helix chain 'A' and resid 1192 through 1194 No H-bonds generated for 'chain 'A' and resid 1192 through 1194' Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1230 through 1239 Processing helix chain 'A' and resid 1249 through 1261 Processing helix chain 'A' and resid 1263 through 1265 No H-bonds generated for 'chain 'A' and resid 1263 through 1265' Processing helix chain 'A' and resid 1269 through 1280 Processing helix chain 'A' and resid 1284 through 1297 removed outlier: 3.570A pdb=" N HIS A1297 " --> pdb=" O ALA A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1315 removed outlier: 4.506A pdb=" N THR A1314 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 3.872A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 31 through 34 No H-bonds generated for 'chain 'C' and resid 31 through 34' Processing helix chain 'C' and resid 109 through 120 Processing sheet with id= A, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.191A pdb=" N ASN A1093 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU A 52 " --> pdb=" O ASN A1093 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL A1095 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 29 through 33 Processing sheet with id= C, first strand: chain 'A' and resid 837 through 840 Processing sheet with id= D, first strand: chain 'A' and resid 1196 through 1199 removed outlier: 7.265A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL A1146 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A1160 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS A1148 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS A1158 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU A1150 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS A1156 " --> pdb=" O GLU A1150 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1210 through 1214 removed outlier: 3.971A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 126 through 128 removed outlier: 3.741A pdb=" N LYS C 127 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR C 39 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 78 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 69 through 72 removed outlier: 3.602A pdb=" N LEU C 71 " --> pdb=" O PHE C 88 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE C 88 " --> pdb=" O LEU C 71 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 972 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 5.63 Time building geometry restraints manager: 6.79 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: 2348 1.32 - 1.44: 4340 1.44 - 1.57: 7714 1.57 - 1.69: 232 1.69 - 1.81: 48 Bond restraints: 14682 Sorted by residual: bond pdb=" C6 GTP B 1 " pdb=" O6 GTP B 1 " ideal model delta sigma weight residual 1.230 1.387 -0.157 2.00e-02 2.50e+03 6.20e+01 bond pdb=" C2 GTP B 1 " pdb=" N2 GTP B 1 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C5 GTP B 1 " pdb=" C6 GTP B 1 " ideal model delta sigma weight residual 1.390 1.458 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O3B GTP B 1 " pdb=" PB GTP B 1 " ideal model delta sigma weight residual 1.610 1.550 0.060 2.00e-02 2.50e+03 9.00e+00 bond pdb=" C2 GTP B 1 " pdb=" N1 GTP B 1 " ideal model delta sigma weight residual 1.380 1.438 -0.058 2.00e-02 2.50e+03 8.37e+00 ... (remaining 14677 not shown) Histogram of bond angle deviations from ideal: 97.22 - 104.61: 615 104.61 - 112.01: 7052 112.01 - 119.40: 5456 119.40 - 126.80: 6880 126.80 - 134.19: 432 Bond angle restraints: 20435 Sorted by residual: angle pdb=" C ASP A 353 " pdb=" N GLN A 354 " pdb=" CA GLN A 354 " ideal model delta sigma weight residual 121.54 131.86 -10.32 1.91e+00 2.74e-01 2.92e+01 angle pdb=" C ASP C 101 " pdb=" N GLU C 102 " pdb=" CA GLU C 102 " ideal model delta sigma weight residual 121.54 131.54 -10.00 1.91e+00 2.74e-01 2.74e+01 angle pdb=" CA THR C 107 " pdb=" CB THR C 107 " pdb=" CG2 THR C 107 " ideal model delta sigma weight residual 110.50 118.04 -7.54 1.70e+00 3.46e-01 1.97e+01 angle pdb=" N GLY A1133 " pdb=" CA GLY A1133 " pdb=" C GLY A1133 " ideal model delta sigma weight residual 110.20 115.93 -5.73 1.32e+00 5.74e-01 1.89e+01 angle pdb=" C3' A B 86 " pdb=" O3' A B 86 " pdb=" P A B 87 " ideal model delta sigma weight residual 120.20 126.65 -6.45 1.50e+00 4.44e-01 1.85e+01 ... (remaining 20430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 8378 35.47 - 70.95: 199 70.95 - 106.42: 20 106.42 - 141.90: 1 141.90 - 177.37: 4 Dihedral angle restraints: 8602 sinusoidal: 4201 harmonic: 4401 Sorted by residual: dihedral pdb=" O4' C B 88 " pdb=" C1' C B 88 " pdb=" N1 C B 88 " pdb=" C2 C B 88 " ideal model delta sinusoidal sigma weight residual 200.00 40.60 159.40 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' U B 7 " pdb=" C1' U B 7 " pdb=" N1 U B 7 " pdb=" C2 U B 7 " ideal model delta sinusoidal sigma weight residual 232.00 56.24 175.76 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA THR C 107 " pdb=" C THR C 107 " pdb=" N GLU C 108 " pdb=" CA GLU C 108 " ideal model delta harmonic sigma weight residual -180.00 -145.35 -34.65 0 5.00e+00 4.00e-02 4.80e+01 ... (remaining 8599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.963: 2409 0.963 - 1.925: 0 1.925 - 2.888: 0 2.888 - 3.851: 0 3.851 - 4.814: 2 Chirality restraints: 2411 Sorted by residual: chirality pdb=" C2' GTP B 1 " pdb=" C1' GTP B 1 " pdb=" C3' GTP B 1 " pdb=" O2' GTP B 1 " both_signs ideal model delta sigma weight residual False -2.47 2.34 -4.81 2.00e-01 2.50e+01 5.79e+02 chirality pdb=" C4' GTP B 1 " pdb=" C3' GTP B 1 " pdb=" C5' GTP B 1 " pdb=" O4' GTP B 1 " both_signs ideal model delta sigma weight residual False -2.47 2.25 -4.72 2.00e-01 2.50e+01 5.58e+02 chirality pdb=" C1' A B 8 " pdb=" O4' A B 8 " pdb=" C2' A B 8 " pdb=" N9 A B 8 " both_signs ideal model delta sigma weight residual False 2.44 2.09 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 2408 not shown) Planarity restraints: 2194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 8 " -0.035 2.00e-02 2.50e+03 1.80e-02 8.94e+00 pdb=" N9 A B 8 " 0.047 2.00e-02 2.50e+03 pdb=" C8 A B 8 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B 8 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 8 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A B 8 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A B 8 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A B 8 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B 8 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 8 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 302 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C LEU A 302 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU A 302 " 0.017 2.00e-02 2.50e+03 pdb=" N SER A 303 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 295 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.07e+00 pdb=" C ASN A 295 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN A 295 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 296 " 0.015 2.00e-02 2.50e+03 ... (remaining 2191 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4123 2.81 - 3.33: 12952 3.33 - 3.86: 24637 3.86 - 4.38: 26604 4.38 - 4.90: 42182 Nonbonded interactions: 110498 Sorted by model distance: nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.290 2.440 nonbonded pdb=" O2' U B 62 " pdb=" OE1 GLN A 402 " model vdw 2.314 2.440 nonbonded pdb=" OG SER A 469 " pdb=" OE1 GLU A 471 " model vdw 2.317 2.440 nonbonded pdb=" O TYR A 136 " pdb=" OG SER A 318 " model vdw 2.319 2.440 nonbonded pdb=" O ARG A 925 " pdb=" OG1 THR A 928 " model vdw 2.328 2.440 ... (remaining 110493 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 P 118 5.49 5 S 26 5.16 5 C 8551 2.51 5 N 2458 2.21 5 O 3022 1.98 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: 0.340 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: 2.740 Check model and map are aligned: 0.230 Convert atoms to be neutral: 0.140 Process input model: 43.920 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 : 0.006 0.157 14682 Z= 0.395 Angle : 1.038 12.694 20435 Z= 0.536 Chirality : 0.148 4.814 2411 Planarity : 0.006 0.052 2194 Dihedral : 14.857 177.369 5754 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.52 (0.17), residues: 1490 helix: -3.23 (0.14), residues: 609 sheet: -1.76 (0.45), residues: 111 loop : -3.02 (0.19), residues: 770 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 240 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 249 average time/residue: 0.2632 time to fit residues: 95.6203 Evaluate side-chains 145 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 1.503 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1212 time to fit residues: 2.6809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 93 optimal weight: 0.1980 chunk 145 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN A 412 HIS A 522 ASN A 674 GLN A 831 ASN A 930 HIS A 980 ASN A 985 HIS A1054 ASN A1093 ASN A1101 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 14682 Z= 0.145 Angle : 0.645 14.107 20435 Z= 0.315 Chirality : 0.039 0.204 2411 Planarity : 0.004 0.041 2194 Dihedral : 14.802 175.232 3012 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -3.32 (0.18), residues: 1490 helix: -1.85 (0.18), residues: 623 sheet: -1.13 (0.50), residues: 98 loop : -2.69 (0.19), residues: 769 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 190 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 12 residues processed: 216 average time/residue: 0.2292 time to fit residues: 75.6789 Evaluate side-chains 150 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 1.531 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1801 time to fit residues: 5.4402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 5.9990 chunk 45 optimal weight: 0.0010 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 157 optimal weight: 20.0000 chunk 129 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 overall best weight: 2.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN A 712 GLN A 739 GLN ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 14682 Z= 0.221 Angle : 0.644 12.593 20435 Z= 0.319 Chirality : 0.040 0.201 2411 Planarity : 0.004 0.037 2194 Dihedral : 14.698 179.768 3012 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -2.69 (0.20), residues: 1490 helix: -1.12 (0.20), residues: 614 sheet: -1.18 (0.50), residues: 100 loop : -2.48 (0.20), residues: 776 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 157 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 14 residues processed: 189 average time/residue: 0.2184 time to fit residues: 64.8639 Evaluate side-chains 146 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.560 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1272 time to fit residues: 5.3841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 14682 Z= 0.214 Angle : 0.627 12.112 20435 Z= 0.309 Chirality : 0.040 0.188 2411 Planarity : 0.004 0.035 2194 Dihedral : 14.579 175.944 3012 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -2.28 (0.21), residues: 1490 helix: -0.73 (0.20), residues: 623 sheet: -0.95 (0.51), residues: 98 loop : -2.31 (0.21), residues: 769 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 179 average time/residue: 0.2219 time to fit residues: 63.5148 Evaluate side-chains 149 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 1.450 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1279 time to fit residues: 4.1513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 131 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 78 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 14682 Z= 0.210 Angle : 0.630 15.176 20435 Z= 0.307 Chirality : 0.039 0.195 2411 Planarity : 0.003 0.036 2194 Dihedral : 14.481 174.059 3012 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -2.02 (0.21), residues: 1490 helix: -0.49 (0.21), residues: 618 sheet: -0.83 (0.52), residues: 98 loop : -2.17 (0.21), residues: 774 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 9 residues processed: 169 average time/residue: 0.2210 time to fit residues: 59.9188 Evaluate side-chains 144 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 1.607 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1347 time to fit residues: 4.3654 ------------------------------------------------------------------------------- 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-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: 61.5364 > 50: distance: 84 - 89: 9.655 distance: 89 - 90: 15.050 distance: 90 - 91: 12.105 distance: 90 - 93: 9.807 distance: 91 - 92: 16.350 distance: 91 - 99: 23.302 distance: 92 - 126: 31.606 distance: 93 - 94: 10.185 distance: 94 - 95: 8.262 distance: 94 - 96: 9.200 distance: 95 - 97: 9.713 distance: 96 - 98: 6.923 distance: 97 - 98: 8.110 distance: 99 - 100: 5.176 distance: 100 - 101: 22.158 distance: 100 - 103: 3.558 distance: 101 - 102: 39.535 distance: 101 - 108: 13.493 distance: 102 - 134: 58.472 distance: 105 - 106: 23.447 distance: 105 - 107: 40.829 distance: 108 - 109: 20.868 distance: 109 - 110: 5.581 distance: 109 - 112: 42.544 distance: 110 - 111: 7.319 distance: 110 - 116: 17.490 distance: 111 - 138: 45.381 distance: 112 - 113: 41.892 distance: 112 - 114: 9.927 distance: 113 - 115: 46.126 distance: 116 - 117: 25.696 distance: 117 - 118: 4.830 distance: 117 - 120: 16.419 distance: 118 - 119: 21.187 distance: 118 - 126: 9.413 distance: 119 - 147: 40.571 distance: 120 - 121: 5.909 distance: 121 - 122: 29.881 distance: 121 - 123: 5.096 distance: 122 - 124: 12.393 distance: 124 - 125: 40.932 distance: 126 - 127: 20.684 distance: 127 - 128: 8.081 distance: 127 - 130: 19.855 distance: 128 - 129: 18.875 distance: 128 - 134: 23.150 distance: 129 - 155: 24.179 distance: 130 - 131: 15.908 distance: 131 - 132: 18.684 distance: 136 - 138: 5.561 distance: 137 - 165: 21.438 distance: 138 - 139: 3.265 distance: 139 - 142: 7.804 distance: 140 - 141: 24.982 distance: 140 - 147: 5.836 distance: 141 - 170: 24.739 distance: 142 - 143: 13.547 distance: 143 - 144: 16.230 distance: 144 - 145: 6.027 distance: 144 - 146: 4.176 distance: 147 - 148: 11.480 distance: 148 - 149: 8.041 distance: 148 - 151: 20.821 distance: 149 - 150: 4.631 distance: 149 - 155: 3.932 distance: 150 - 177: 12.854 distance: 151 - 152: 22.077 distance: 152 - 153: 24.484 distance: 152 - 154: 19.588 distance: 155 - 156: 5.863 distance: 156 - 157: 10.338 distance: 156 - 159: 9.318 distance: 157 - 158: 10.762 distance: 157 - 165: 5.371 distance: 158 - 185: 21.209 distance: 159 - 160: 19.570 distance: 160 - 162: 9.549 distance: 161 - 163: 11.680 distance: 162 - 164: 13.957 distance: 163 - 164: 6.057 distance: 165 - 166: 4.735 distance: 166 - 167: 7.883 distance: 166 - 169: 15.897 distance: 167 - 168: 25.539 distance: 167 - 170: 19.214