Starting phenix.real_space_refine on Mon Mar 18 19:58:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga8_29892/03_2024/8ga8_29892.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga8_29892/03_2024/8ga8_29892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga8_29892/03_2024/8ga8_29892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga8_29892/03_2024/8ga8_29892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga8_29892/03_2024/8ga8_29892.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga8_29892/03_2024/8ga8_29892.pdb" } resolution = 3.5 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= 0.001 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 95 5.16 5 C 14023 2.51 5 N 3795 2.21 5 O 4096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 37": "OD1" <-> "OD2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "A ASP 695": "OD1" <-> "OD2" Residue "A ASP 707": "OD1" <-> "OD2" Residue "A ASP 762": "OD1" <-> "OD2" Residue "A TYR 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1243": "OD1" <-> "OD2" Residue "J ASP 122": "OD1" <-> "OD2" Residue "J ASP 161": "OD1" <-> "OD2" Residue "J PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 95": "OD1" <-> "OD2" Residue "L GLU 109": "OE1" <-> "OE2" Residue "M GLU 56": "OE1" <-> "OE2" Residue "M TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 204": "OE1" <-> "OE2" Residue "M TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 288": "OD1" <-> "OD2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 370": "OD1" <-> "OD2" Residue "K PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 818": "OD1" <-> "OD2" Residue "D GLU 904": "OE1" <-> "OE2" Residue "D PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1226": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22011 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1206 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "A" Number of atoms: 4417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4417 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain breaks: 5 Chain: "J" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 767 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "L" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1052 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 1 Chain: "M" Number of atoms: 1832 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 223, 1824 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 223, 1824 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 4 bond proxies already assigned to first conformer: 1839 Chain: "G" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 838 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain breaks: 1 Chain: "B" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3039 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "E" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3031 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 18, 'TRANS': 363} Chain: "K" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1587 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 14, 'TRANS': 184} Chain breaks: 1 Chain: "D" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4240 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 12, 'TRANS': 490} Chain breaks: 5 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AILE M 169 " occ=0.51 ... (14 atoms not shown) pdb=" CD1BILE M 169 " occ=0.49 Time building chain proxies: 12.50, per 1000 atoms: 0.57 Number of scatterers: 22011 At special positions: 0 Unit cell: (104.076, 156.94, 199.892, 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) Zn 2 29.99 S 95 16.00 O 4096 8.00 N 3795 7.00 C 14023 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: 8.88 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" ND1 HIS E 188 " 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5104 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 11 sheets defined 61.8% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'H' and resid 11 through 35 removed outlier: 4.057A pdb=" N ARG H 17 " --> pdb=" O ARG H 13 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 56 removed outlier: 3.855A pdb=" N GLN H 56 " --> pdb=" O THR H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 117 Processing helix chain 'H' and resid 300 through 316 removed outlier: 3.873A pdb=" N GLU H 306 " --> pdb=" O ASP H 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 677 removed outlier: 3.647A pdb=" N GLU A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 694 Processing helix chain 'A' and resid 698 through 707 Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 759 through 764 removed outlier: 4.285A pdb=" N PHE A 764 " --> pdb=" O LYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.920A pdb=" N GLU A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 777 " --> pdb=" O MET A 773 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 772 through 777' Processing helix chain 'A' and resid 803 through 839 removed outlier: 3.677A pdb=" N THR A 833 " --> pdb=" O GLN A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 841 No H-bonds generated for 'chain 'A' and resid 840 through 841' Processing helix chain 'A' and resid 842 through 846 Processing helix chain 'A' and resid 861 through 871 removed outlier: 3.587A pdb=" N VAL A 866 " --> pdb=" O ILE A 862 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 867 " --> pdb=" O TYR A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 886 removed outlier: 3.778A pdb=" N ILE A 879 " --> pdb=" O ARG A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 922 Proline residue: A 892 - end of helix removed outlier: 3.990A pdb=" N LYS A 914 " --> pdb=" O ARG A 910 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 929 removed outlier: 3.636A pdb=" N LEU A 928 " --> pdb=" O PHE A 924 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 929 " --> pdb=" O PHE A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 943 removed outlier: 3.524A pdb=" N LEU A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 961 removed outlier: 3.689A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 955 " --> pdb=" O GLU A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 999 removed outlier: 4.374A pdb=" N ASP A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 988 " --> pdb=" O ILE A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1023 Processing helix chain 'A' and resid 1066 through 1070 removed outlier: 3.795A pdb=" N HIS A1070 " --> pdb=" O LEU A1066 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1066 through 1070' Processing helix chain 'A' and resid 1070 through 1082 Processing helix chain 'A' and resid 1141 through 1163 removed outlier: 4.265A pdb=" N PHE A1147 " --> pdb=" O ASN A1143 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A1161 " --> pdb=" O ARG A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1175 removed outlier: 3.811A pdb=" N LYS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1202 through 1216 removed outlier: 3.869A pdb=" N ARG A1209 " --> pdb=" O LYS A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1233 removed outlier: 3.715A pdb=" N PHE A1224 " --> pdb=" O GLU A1220 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU A1225 " --> pdb=" O HIS A1221 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU A1226 " --> pdb=" O GLN A1222 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA A1231 " --> pdb=" O SER A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1259 Processing helix chain 'A' and resid 1259 through 1274 removed outlier: 3.590A pdb=" N ASN A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1294 removed outlier: 3.744A pdb=" N HIS A1293 " --> pdb=" O GLN A1289 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 120 removed outlier: 3.538A pdb=" N LEU J 112 " --> pdb=" O THR J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 135 removed outlier: 3.971A pdb=" N GLY J 135 " --> pdb=" O GLY J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 141 Processing helix chain 'J' and resid 142 through 148 Processing helix chain 'J' and resid 158 through 173 removed outlier: 3.732A pdb=" N LEU J 162 " --> pdb=" O HIS J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 191 Proline residue: J 182 - end of helix Processing helix chain 'L' and resid 13 through 39 Proline residue: L 22 - end of helix removed outlier: 3.648A pdb=" N CYS L 39 " --> pdb=" O ILE L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 54 Processing helix chain 'L' and resid 61 through 114 Proline residue: L 81 - end of helix removed outlier: 4.174A pdb=" N ASN L 114 " --> pdb=" O VAL L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 152 removed outlier: 3.554A pdb=" N GLU L 136 " --> pdb=" O HIS L 132 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER L 150 " --> pdb=" O ASN L 146 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN L 151 " --> pdb=" O SER L 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 37 removed outlier: 4.240A pdb=" N GLU M 36 " --> pdb=" O ARG M 32 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS M 37 " --> pdb=" O ILE M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 156 through 160 Processing helix chain 'M' and resid 162 through 166 Processing helix chain 'M' and resid 180 through 186 Processing helix chain 'M' and resid 188 through 217 removed outlier: 3.773A pdb=" N SER M 207 " --> pdb=" O LYS M 203 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 232 removed outlier: 3.624A pdb=" N ASN M 232 " --> pdb=" O GLU M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 329 through 384 removed outlier: 3.518A pdb=" N LEU M 384 " --> pdb=" O SER M 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 298 removed outlier: 3.620A pdb=" N ASP G 297 " --> pdb=" O ARG G 293 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE G 298 " --> pdb=" O ARG G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 404 removed outlier: 3.577A pdb=" N PHE G 400 " --> pdb=" O ILE G 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.893A pdb=" N ASN B 31 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 42 through 55 removed outlier: 4.358A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.554A pdb=" N LYS B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET B 61 " --> pdb=" O TYR B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 97 through 105 Processing helix chain 'B' and resid 115 through 136 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.930A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 287 through 300 removed outlier: 3.909A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 42 through 56 removed outlier: 3.731A pdb=" N ARG E 46 " --> pdb=" O PRO E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 75 Processing helix chain 'E' and resid 79 through 89 Processing helix chain 'E' and resid 97 through 105 Processing helix chain 'E' and resid 115 through 136 Processing helix chain 'E' and resid 164 through 175 removed outlier: 3.673A pdb=" N LEU E 168 " --> pdb=" O ASN E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 196 Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 243 through 262 Proline residue: E 253 - end of helix Processing helix chain 'E' and resid 287 through 300 removed outlier: 3.911A pdb=" N CYS E 294 " --> pdb=" O GLY E 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL E 295 " --> pdb=" O HIS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 330 removed outlier: 3.642A pdb=" N ASN E 330 " --> pdb=" O THR E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 347 Processing helix chain 'E' and resid 365 through 381 Processing helix chain 'K' and resid 70 through 80 Processing helix chain 'K' and resid 131 through 135 Processing helix chain 'K' and resid 144 through 153 removed outlier: 3.624A pdb=" N ASN K 153 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 163 Processing helix chain 'K' and resid 176 through 184 Processing helix chain 'D' and resid 662 through 677 Processing helix chain 'D' and resid 678 through 694 Processing helix chain 'D' and resid 698 through 710 removed outlier: 3.869A pdb=" N PHE D 708 " --> pdb=" O GLU D 704 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR D 709 " --> pdb=" O LYS D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 724 Processing helix chain 'D' and resid 760 through 764 removed outlier: 3.539A pdb=" N THR D 763 " --> pdb=" O LYS D 760 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE D 764 " --> pdb=" O SER D 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 760 through 764' Processing helix chain 'D' and resid 771 through 778 Processing helix chain 'D' and resid 801 through 841 removed outlier: 4.002A pdb=" N ASN D 840 " --> pdb=" O ASN D 836 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET D 841 " --> pdb=" O LYS D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 848 removed outlier: 3.523A pdb=" N ASN D 848 " --> pdb=" O ASN D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 871 removed outlier: 3.775A pdb=" N LYS D 865 " --> pdb=" O THR D 861 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL D 866 " --> pdb=" O ILE D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 886 removed outlier: 4.444A pdb=" N PHE D 877 " --> pdb=" O LYS D 873 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU D 878 " --> pdb=" O GLU D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 924 Proline residue: D 892 - end of helix removed outlier: 3.515A pdb=" N GLU D 903 " --> pdb=" O LYS D 899 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS D 914 " --> pdb=" O ARG D 910 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL D 915 " --> pdb=" O GLU D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 943 removed outlier: 3.940A pdb=" N LYS D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 943 " --> pdb=" O ASP D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 960 removed outlier: 3.602A pdb=" N LEU D 948 " --> pdb=" O THR D 944 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE D 949 " --> pdb=" O THR D 945 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 999 removed outlier: 4.379A pdb=" N TYR D 986 " --> pdb=" O LYS D 982 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP D 987 " --> pdb=" O ASN D 983 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE D 988 " --> pdb=" O ILE D 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 1003 through 1023 removed outlier: 3.504A pdb=" N ARG D1009 " --> pdb=" O PRO D1005 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP D1012 " --> pdb=" O GLU D1008 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU D1014 " --> pdb=" O LEU D1010 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYS D1015 " --> pdb=" O LYS D1011 " (cutoff:3.500A) Processing helix chain 'D' and resid 1066 through 1070 Processing helix chain 'D' and resid 1141 through 1160 removed outlier: 3.718A pdb=" N ARG D1157 " --> pdb=" O THR D1153 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D1158 " --> pdb=" O ILE D1154 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D1160 " --> pdb=" O GLU D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1161 through 1163 No H-bonds generated for 'chain 'D' and resid 1161 through 1163' Processing helix chain 'D' and resid 1164 through 1173 removed outlier: 4.000A pdb=" N ASN D1173 " --> pdb=" O THR D1169 " (cutoff:3.500A) Processing helix chain 'D' and resid 1204 through 1216 removed outlier: 3.682A pdb=" N ARG D1213 " --> pdb=" O ARG D1209 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU D1214 " --> pdb=" O LEU D1210 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE D1215 " --> pdb=" O SER D1211 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN D1216 " --> pdb=" O ARG D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1232 removed outlier: 4.271A pdb=" N PHE D1224 " --> pdb=" O GLU D1220 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU D1225 " --> pdb=" O HIS D1221 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU D1226 " --> pdb=" O GLN D1222 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D1228 " --> pdb=" O PHE D1224 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG D1229 " --> pdb=" O GLU D1225 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN D1230 " --> pdb=" O GLU D1226 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA D1231 " --> pdb=" O SER D1227 " (cutoff:3.500A) Processing helix chain 'D' and resid 1241 through 1259 removed outlier: 3.568A pdb=" N ASP D1259 " --> pdb=" O THR D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1259 through 1274 Processing helix chain 'D' and resid 1279 through 1293 removed outlier: 3.718A pdb=" N ILE D1284 " --> pdb=" O ALA D1280 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS D1293 " --> pdb=" O GLN D1289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 750 through 751 removed outlier: 4.268A pdb=" N TYR A 755 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AA3, first strand: chain 'M' and resid 89 through 90 removed outlier: 4.001A pdb=" N GLN M 89 " --> pdb=" O LEU M 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 24 Processing sheet with id=AA5, first strand: chain 'B' and resid 203 through 206 removed outlier: 6.758A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 62 through 64 removed outlier: 6.732A pdb=" N VAL E 21 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N TYR E 64 " --> pdb=" O VAL E 21 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR E 23 " --> pdb=" O TYR E 64 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA E 142 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU E 181 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLN E 270 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE E 183 " --> pdb=" O GLN E 270 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 90 through 91 removed outlier: 6.267A pdb=" N LEU K 90 " --> pdb=" O LYS K 142 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASP K 225 " --> pdb=" O ILE K 272 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE K 272 " --> pdb=" O ASP K 225 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU K 227 " --> pdb=" O ILE K 270 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE K 270 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU K 229 " --> pdb=" O TYR K 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 90 through 91 removed outlier: 6.267A pdb=" N LEU K 90 " --> pdb=" O LYS K 142 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASP K 225 " --> pdb=" O ILE K 272 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE K 272 " --> pdb=" O ASP K 225 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU K 227 " --> pdb=" O ILE K 270 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE K 270 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU K 229 " --> pdb=" O TYR K 268 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 243 through 244 Processing sheet with id=AB1, first strand: chain 'D' and resid 755 through 757 Processing sheet with id=AB2, first strand: chain 'D' and resid 975 through 978 removed outlier: 3.794A pdb=" N LEU D 975 " --> pdb=" O ILE D1314 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D1314 " --> pdb=" O LEU D 975 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE D1301 " --> pdb=" O ALA D1140 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA D1140 " --> pdb=" O PHE D1301 " (cutoff:3.500A) 1177 hydrogen bonds defined for protein. 3450 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: 6.30 Time building geometry restraints manager: 9.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5886 1.33 - 1.45: 4045 1.45 - 1.57: 12394 1.57 - 1.69: 1 1.69 - 1.81: 155 Bond restraints: 22481 Sorted by residual: bond pdb=" CB PRO B 111 " pdb=" CG PRO B 111 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.33e+00 bond pdb=" CB GLU M 36 " pdb=" CG GLU M 36 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.20e+00 bond pdb=" CG PRO B 111 " pdb=" CD PRO B 111 " ideal model delta sigma weight residual 1.503 1.553 -0.050 3.40e-02 8.65e+02 2.17e+00 bond pdb=" CB GLN D1222 " pdb=" CG GLN D1222 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" CB GLU A 843 " pdb=" CG GLU A 843 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.55e+00 ... (remaining 22476 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.86: 386 105.86 - 112.93: 11922 112.93 - 119.99: 7964 119.99 - 127.05: 9817 127.05 - 134.12: 228 Bond angle restraints: 30317 Sorted by residual: angle pdb=" CA PRO B 111 " pdb=" N PRO B 111 " pdb=" CD PRO B 111 " ideal model delta sigma weight residual 112.00 103.47 8.53 1.40e+00 5.10e-01 3.71e+01 angle pdb=" CA GLU M 36 " pdb=" CB GLU M 36 " pdb=" CG GLU M 36 " ideal model delta sigma weight residual 114.10 121.30 -7.20 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CA PRO B 253 " pdb=" N PRO B 253 " pdb=" CD PRO B 253 " ideal model delta sigma weight residual 112.00 107.05 4.95 1.40e+00 5.10e-01 1.25e+01 angle pdb=" N PHE D1017 " pdb=" CA PHE D1017 " pdb=" CB PHE D1017 " ideal model delta sigma weight residual 110.16 115.18 -5.02 1.48e+00 4.57e-01 1.15e+01 angle pdb=" CB GLU M 36 " pdb=" CG GLU M 36 " pdb=" CD GLU M 36 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.70e+00 3.46e-01 1.06e+01 ... (remaining 30312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11394 17.97 - 35.94: 1702 35.94 - 53.91: 406 53.91 - 71.88: 62 71.88 - 89.85: 21 Dihedral angle restraints: 13585 sinusoidal: 5698 harmonic: 7887 Sorted by residual: dihedral pdb=" CA TYR B 346 " pdb=" C TYR B 346 " pdb=" N TYR B 347 " pdb=" CA TYR B 347 " ideal model delta harmonic sigma weight residual -180.00 -161.32 -18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA TYR E 313 " pdb=" C TYR E 313 " pdb=" N THR E 314 " pdb=" CA THR E 314 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP A 695 " pdb=" CB ASP A 695 " pdb=" CG ASP A 695 " pdb=" OD1 ASP A 695 " ideal model delta sinusoidal sigma weight residual -30.00 -89.77 59.77 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 13582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2427 0.040 - 0.079: 685 0.079 - 0.119: 152 0.119 - 0.158: 15 0.158 - 0.198: 3 Chirality restraints: 3282 Sorted by residual: chirality pdb=" CA MET L 80 " pdb=" N MET L 80 " pdb=" C MET L 80 " pdb=" CB MET L 80 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA PHE A1180 " pdb=" N PHE A1180 " pdb=" C PHE A1180 " pdb=" CB PHE A1180 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA GLU L 105 " pdb=" N GLU L 105 " pdb=" C GLU L 105 " pdb=" CB GLU L 105 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 3279 not shown) Planarity restraints: 3894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 252 " -0.073 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO B 253 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO B 253 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 253 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 110 " 0.049 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO B 111 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 111 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 111 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 90 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO B 91 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 91 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 91 " 0.028 5.00e-02 4.00e+02 ... (remaining 3891 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 264 2.60 - 3.18: 19004 3.18 - 3.75: 36049 3.75 - 4.33: 45415 4.33 - 4.90: 75987 Nonbonded interactions: 176719 Sorted by model distance: nonbonded pdb=" OD1 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.028 2.230 nonbonded pdb=" OD1 ASP E 186 " pdb="ZN ZN E 501 " model vdw 2.031 2.230 nonbonded pdb=" OD2 ASP E 274 " pdb="ZN ZN E 501 " model vdw 2.035 2.230 nonbonded pdb=" OD2 ASP B 274 " pdb="ZN ZN B 501 " model vdw 2.041 2.230 nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.074 2.230 ... (remaining 176714 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' and (resid 659 through 724 or resid 749 through 787 or resid 799 thro \ ugh 1070 or resid 1075 or resid 1079 through 1080 or resid 1135 through 1174 or \ resid 1203 through 1317)) selection = (chain 'D' and (resid 659 through 724 or resid 749 through 787 or resid 799 thro \ ugh 961 or resid 975 through 1070 or resid 1131 or resid 1133 through 1317)) } ncs_group { reference = (chain 'B' and (resid 2 through 383 or resid 501)) selection = chain 'E' } 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=0.49 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.820 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 61.770 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.100 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: 0.010 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: 73.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 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 0.126 22481 Z= 0.166 Angle : 0.540 11.010 30317 Z= 0.281 Chirality : 0.038 0.198 3282 Planarity : 0.004 0.109 3894 Dihedral : 17.426 89.848 8481 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.33 % Allowed : 29.89 % Favored : 69.78 % 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: 0.98 (0.17), residues: 2622 helix: 1.76 (0.13), residues: 1496 sheet: -0.52 (0.39), residues: 204 loop : -0.90 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D1151 HIS 0.009 0.001 HIS H 106 PHE 0.019 0.001 PHE H 19 TYR 0.021 0.001 TYR B 58 ARG 0.006 0.000 ARG D1229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 240 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 841 MET cc_start: 0.6086 (tmm) cc_final: 0.5029 (tmm) REVERT: D 1222 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8551 (tm-30) REVERT: D 1226 GLU cc_start: 0.8132 (pp20) cc_final: 0.7926 (pp20) outliers start: 8 outliers final: 5 residues processed: 243 average time/residue: 0.3303 time to fit residues: 125.1246 Evaluate side-chains 231 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 226 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 928 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 50.1661 > 50: distance: 141 - 154: 3.105 distance: 165 - 170: 12.621 distance: 170 - 171: 8.406 distance: 171 - 172: 12.120 distance: 171 - 174: 8.590 distance: 172 - 173: 11.448 distance: 172 - 178: 10.463 distance: 174 - 175: 8.987 distance: 175 - 176: 12.741 distance: 175 - 177: 14.097 distance: 178 - 179: 17.939 distance: 179 - 180: 19.853 distance: 179 - 182: 10.805 distance: 180 - 181: 10.920 distance: 180 - 190: 19.698 distance: 182 - 183: 12.360 distance: 183 - 184: 15.604 distance: 183 - 185: 10.757 distance: 184 - 186: 8.233 distance: 185 - 187: 11.828 distance: 186 - 188: 5.465 distance: 187 - 188: 9.513 distance: 188 - 189: 10.555 distance: 190 - 191: 8.417 distance: 191 - 192: 16.732 distance: 191 - 194: 13.149 distance: 192 - 193: 12.820 distance: 192 - 199: 18.973 distance: 194 - 195: 8.539 distance: 195 - 196: 6.200 distance: 196 - 197: 9.293 distance: 197 - 198: 7.513 distance: 199 - 200: 10.282 distance: 200 - 201: 9.090 distance: 200 - 203: 10.066 distance: 201 - 202: 3.776 distance: 203 - 204: 6.177 distance: 204 - 205: 10.480 distance: 204 - 206: 9.103 distance: 207 - 208: 5.065 distance: 208 - 209: 10.274 distance: 208 - 211: 4.712 distance: 209 - 210: 17.111 distance: 209 - 213: 7.172 distance: 211 - 212: 13.143 distance: 213 - 214: 4.667 distance: 214 - 215: 5.122 distance: 214 - 217: 11.733 distance: 215 - 216: 25.103 distance: 215 - 220: 19.037 distance: 217 - 218: 6.462 distance: 217 - 219: 14.937 distance: 220 - 221: 12.901 distance: 221 - 222: 27.240 distance: 221 - 224: 18.945 distance: 222 - 223: 13.098 distance: 222 - 231: 13.944 distance: 224 - 225: 19.708 distance: 225 - 226: 24.003 distance: 226 - 227: 10.393 distance: 227 - 228: 4.090 distance: 228 - 229: 7.473 distance: 228 - 230: 9.306 distance: 231 - 232: 13.888 distance: 231 - 237: 30.152 distance: 232 - 233: 23.506 distance: 232 - 235: 13.887 distance: 233 - 234: 11.842 distance: 233 - 238: 28.696 distance: 235 - 236: 3.691 distance: 236 - 237: 40.998 distance: 238 - 239: 24.681 distance: 239 - 240: 19.750 distance: 239 - 242: 17.682 distance: 240 - 241: 5.090 distance: 240 - 244: 7.612 distance: 242 - 243: 24.306 distance: 244 - 245: 20.412 distance: 245 - 246: 7.599 distance: 245 - 248: 17.356 distance: 246 - 247: 11.426 distance: 246 - 252: 11.984 distance: 248 - 249: 17.473 distance: 249 - 250: 15.458 distance: 249 - 251: 23.227