Starting phenix.real_space_refine on Thu Dec 14 19:01:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/12_2023/7xg3_33184_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/12_2023/7xg3_33184.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/12_2023/7xg3_33184_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/12_2023/7xg3_33184_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/12_2023/7xg3_33184_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/12_2023/7xg3_33184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/12_2023/7xg3_33184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/12_2023/7xg3_33184_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/12_2023/7xg3_33184_updated.pdb" } resolution = 3.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4742 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 127 5.49 5 S 105 5.16 5 C 14965 2.51 5 N 4317 2.21 5 O 4853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 194": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 84": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 328": "OE1" <-> "OE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "G GLU 120": "OE1" <-> "OE2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G GLU 320": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "H ARG 207": "NH1" <-> "NH2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L GLU 142": "OE1" <-> "OE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L ARG 557": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 24368 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1897 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "B" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1709 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 17, 'TRANS': 201} Chain: "C" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2482 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 18, 'TRANS': 309} Chain breaks: 1 Chain: "D" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2485 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 18, 'TRANS': 310} Chain breaks: 1 Chain: "E" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2445 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain breaks: 1 Chain: "F" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2437 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 18, 'TRANS': 303} Chain breaks: 1 Chain: "G" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1899 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 13, 'TRANS': 235} Chain breaks: 2 Chain: "H" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1800 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 9, 'TRANS': 224} Chain: "I" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1317 Classifications: {'RNA': 61} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 13, 'rna3p_pur': 26, 'rna3p_pyr': 11} Link IDs: {'rna2p': 23, 'rna3p': 37} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "J" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 616 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "L" Number of atoms: 4542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4542 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 31, 'TRANS': 562} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 248 SG CYS A 33 37.545 91.107 19.864 1.00 60.29 S Time building chain proxies: 13.63, per 1000 atoms: 0.56 Number of scatterers: 24368 At special positions: 0 Unit cell: (107.8, 140.8, 178.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 105 16.00 P 127 15.00 O 4853 8.00 N 4317 7.00 C 14965 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: 10.38 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 33 " 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 29 sheets defined 32.9% alpha, 14.2% beta 27 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 11.38 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.620A pdb=" N ASP A 9 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN A 10 " --> pdb=" O ILE A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 97 through 103 Processing helix chain 'A' and resid 150 through 163 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 209 through 218 removed outlier: 3.796A pdb=" N TYR A 217 " --> pdb=" O TRP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'B' and resid 23 through 38 Processing helix chain 'B' and resid 45 through 48 No H-bonds generated for 'chain 'B' and resid 45 through 48' Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'C' and resid 67 through 81 Processing helix chain 'C' and resid 83 through 90 Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.632A pdb=" N GLU C 157 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ARG C 158 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 160 " --> pdb=" O GLU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 194 No H-bonds generated for 'chain 'C' and resid 191 through 194' Processing helix chain 'C' and resid 201 through 222 Processing helix chain 'C' and resid 269 through 284 removed outlier: 5.117A pdb=" N THR C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 332 removed outlier: 3.689A pdb=" N GLY C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'D' and resid 67 through 81 Processing helix chain 'D' and resid 83 through 88 Processing helix chain 'D' and resid 96 through 104 Processing helix chain 'D' and resid 118 through 125 Processing helix chain 'D' and resid 154 through 156 No H-bonds generated for 'chain 'D' and resid 154 through 156' Processing helix chain 'D' and resid 184 through 186 No H-bonds generated for 'chain 'D' and resid 184 through 186' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 201 through 221 Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 320 through 331 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'E' and resid 67 through 79 Processing helix chain 'E' and resid 83 through 89 Processing helix chain 'E' and resid 96 through 103 Processing helix chain 'E' and resid 118 through 125 Processing helix chain 'E' and resid 130 through 133 No H-bonds generated for 'chain 'E' and resid 130 through 133' Processing helix chain 'E' and resid 155 through 157 No H-bonds generated for 'chain 'E' and resid 155 through 157' Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'E' and resid 269 through 280 Processing helix chain 'E' and resid 320 through 330 Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'F' and resid 67 through 81 Processing helix chain 'F' and resid 84 through 89 Processing helix chain 'F' and resid 96 through 103 Processing helix chain 'F' and resid 118 through 124 Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 201 through 215 Processing helix chain 'F' and resid 269 through 280 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 320 through 330 Processing helix chain 'F' and resid 336 through 342 Processing helix chain 'G' and resid 67 through 80 Processing helix chain 'G' and resid 83 through 88 Processing helix chain 'G' and resid 96 through 103 Processing helix chain 'G' and resid 118 through 125 Processing helix chain 'G' and resid 154 through 158 Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 269 through 284 removed outlier: 4.869A pdb=" N THR G 283 " --> pdb=" O LEU G 279 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN G 284 " --> pdb=" O ASN G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 331 Processing helix chain 'G' and resid 336 through 342 Processing helix chain 'H' and resid 16 through 26 Processing helix chain 'H' and resid 32 through 38 Processing helix chain 'H' and resid 70 through 94 Proline residue: H 82 - end of helix Processing helix chain 'H' and resid 132 through 139 Processing helix chain 'H' and resid 142 through 163 removed outlier: 4.068A pdb=" N VAL H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE H 147 " --> pdb=" O THR H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 230 No H-bonds generated for 'chain 'H' and resid 227 through 230' Processing helix chain 'L' and resid 11 through 13 No H-bonds generated for 'chain 'L' and resid 11 through 13' Processing helix chain 'L' and resid 19 through 30 Processing helix chain 'L' and resid 41 through 43 No H-bonds generated for 'chain 'L' and resid 41 through 43' Processing helix chain 'L' and resid 45 through 59 removed outlier: 4.045A pdb=" N LYS L 59 " --> pdb=" O ALA L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 77 removed outlier: 4.391A pdb=" N TRP L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN L 74 " --> pdb=" O ALA L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 88 Processing helix chain 'L' and resid 96 through 98 No H-bonds generated for 'chain 'L' and resid 96 through 98' Processing helix chain 'L' and resid 102 through 111 Processing helix chain 'L' and resid 115 through 121 Processing helix chain 'L' and resid 130 through 139 Processing helix chain 'L' and resid 147 through 153 removed outlier: 3.752A pdb=" N LEU L 153 " --> pdb=" O ASP L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 186 removed outlier: 4.266A pdb=" N SER L 183 " --> pdb=" O VAL L 179 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN L 184 " --> pdb=" O ALA L 180 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR L 185 " --> pdb=" O MET L 181 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR L 186 " --> pdb=" O ARG L 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 207 Processing helix chain 'L' and resid 238 through 248 removed outlier: 4.692A pdb=" N GLU L 242 " --> pdb=" O HIS L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 263 Processing helix chain 'L' and resid 275 through 286 removed outlier: 4.009A pdb=" N VAL L 286 " --> pdb=" O THR L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 318 Processing helix chain 'L' and resid 329 through 344 Processing helix chain 'L' and resid 371 through 378 Processing helix chain 'L' and resid 399 through 404 Processing helix chain 'L' and resid 421 through 425 removed outlier: 3.687A pdb=" N ALA L 425 " --> pdb=" O TRP L 422 " (cutoff:3.500A) Processing helix chain 'L' and resid 442 through 458 Processing helix chain 'L' and resid 470 through 487 removed outlier: 5.603A pdb=" N ALA L 482 " --> pdb=" O GLY L 478 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALA L 483 " --> pdb=" O ARG L 479 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ASP L 486 " --> pdb=" O ALA L 482 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ARG L 487 " --> pdb=" O ALA L 483 " (cutoff:3.500A) Processing helix chain 'L' and resid 497 through 509 Processing helix chain 'L' and resid 520 through 522 No H-bonds generated for 'chain 'L' and resid 520 through 522' Processing helix chain 'L' and resid 537 through 539 No H-bonds generated for 'chain 'L' and resid 537 through 539' Processing helix chain 'L' and resid 559 through 568 Processing helix chain 'L' and resid 570 through 587 removed outlier: 4.000A pdb=" N ARG L 587 " --> pdb=" O GLN L 583 " (cutoff:3.500A) Processing helix chain 'L' and resid 614 through 622 Processing sheet with id= A, first strand: chain 'A' and resid 43 through 45 Processing sheet with id= B, first strand: chain 'A' and resid 91 through 93 removed outlier: 6.443A pdb=" N HIS A 138 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 114 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 72 through 75 removed outlier: 6.527A pdb=" N ALA B 128 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU B 10 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 55 through 58 removed outlier: 4.580A pdb=" N GLU B 55 " --> pdb=" O LYS B 67 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 80 through 86 Processing sheet with id= F, first strand: chain 'B' and resid 196 through 200 Processing sheet with id= G, first strand: chain 'C' and resid 144 through 146 removed outlier: 6.478A pdb=" N ARG C 8 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ILE C 300 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 45 through 50 Processing sheet with id= I, first strand: chain 'C' and resid 174 through 181 Processing sheet with id= J, first strand: chain 'D' and resid 144 through 146 removed outlier: 5.955A pdb=" N ARG D 8 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE D 300 " --> pdb=" O ARG D 8 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 45 through 51 Processing sheet with id= L, first strand: chain 'D' and resid 174 through 181 Processing sheet with id= M, first strand: chain 'E' and resid 144 through 146 removed outlier: 6.298A pdb=" N ARG E 8 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE E 300 " --> pdb=" O ARG E 8 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 21 through 23 Processing sheet with id= O, first strand: chain 'E' and resid 45 through 51 Processing sheet with id= P, first strand: chain 'E' and resid 174 through 181 Processing sheet with id= Q, first strand: chain 'F' and resid 144 through 146 removed outlier: 6.055A pdb=" N ARG F 8 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE F 300 " --> pdb=" O ARG F 8 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 20 through 23 Processing sheet with id= S, first strand: chain 'F' and resid 45 through 51 Processing sheet with id= T, first strand: chain 'F' and resid 174 through 180 Processing sheet with id= U, first strand: chain 'G' and resid 298 through 301 removed outlier: 3.755A pdb=" N THR G 6 " --> pdb=" O ASP G 301 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 45 through 50 Processing sheet with id= W, first strand: chain 'H' and resid 102 through 109 removed outlier: 3.748A pdb=" N PHE H 60 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA H 65 " --> pdb=" O SER H 58 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 112 through 114 removed outlier: 4.024A pdb=" N GLU H 113 " --> pdb=" O ARG H 207 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.995A pdb=" N GLY H 177 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU H 203 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE H 175 " --> pdb=" O GLU H 203 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 180 through 185 Processing sheet with id= AA, first strand: chain 'L' and resid 412 through 414 removed outlier: 6.289A pdb=" N ILE L 34 " --> pdb=" O ALA L 413 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA L 384 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA L 37 " --> pdb=" O ALA L 384 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU L 386 " --> pdb=" O ALA L 37 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 251 through 254 Processing sheet with id= AC, first strand: chain 'L' and resid 427 through 429 removed outlier: 6.681A pdb=" N LYS L 597 " --> pdb=" O LEU L 428 " (cutoff:3.500A) 764 hydrogen bonds defined for protein. 2169 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 7.62 Time building geometry restraints manager: 11.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4443 1.33 - 1.45: 6765 1.45 - 1.57: 13472 1.57 - 1.70: 257 1.70 - 1.82: 193 Bond restraints: 25130 Sorted by residual: bond pdb=" O3' 23G I 61 " pdb=" PC 23G I 61 " ideal model delta sigma weight residual 1.334 1.604 -0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C4' 23G I 61 " pdb=" O4' 23G I 61 " ideal model delta sigma weight residual 1.663 1.429 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C4' 23G I 61 " pdb=" C3' 23G I 61 " ideal model delta sigma weight residual 1.302 1.517 -0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C2' 23G I 61 " pdb=" O2' 23G I 61 " ideal model delta sigma weight residual 1.250 1.427 -0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" N3 23G I 61 " pdb=" C4 23G I 61 " ideal model delta sigma weight residual 1.502 1.354 0.148 2.00e-02 2.50e+03 5.48e+01 ... (remaining 25125 not shown) Histogram of bond angle deviations from ideal: 94.00 - 102.41: 198 102.41 - 110.82: 9018 110.82 - 119.24: 12681 119.24 - 127.65: 12361 127.65 - 136.06: 413 Bond angle restraints: 34671 Sorted by residual: angle pdb=" C3' G I 26 " pdb=" C2' G I 26 " pdb=" O2' G I 26 " ideal model delta sigma weight residual 114.60 124.72 -10.12 1.50e+00 4.44e-01 4.55e+01 angle pdb=" C4' U I 21 " pdb=" C3' U I 21 " pdb=" O3' U I 21 " ideal model delta sigma weight residual 109.40 119.00 -9.60 1.50e+00 4.44e-01 4.10e+01 angle pdb=" C4' A I 27 " pdb=" C3' A I 27 " pdb=" O3' A I 27 " ideal model delta sigma weight residual 109.40 100.31 9.09 1.50e+00 4.44e-01 3.67e+01 angle pdb=" C4' DC K 23 " pdb=" C3' DC K 23 " pdb=" O3' DC K 23 " ideal model delta sigma weight residual 110.00 118.69 -8.69 1.50e+00 4.44e-01 3.36e+01 angle pdb=" O3' G I 26 " pdb=" C3' G I 26 " pdb=" C2' G I 26 " ideal model delta sigma weight residual 109.50 117.94 -8.44 1.50e+00 4.44e-01 3.17e+01 ... (remaining 34666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 14145 35.95 - 71.91: 711 71.91 - 107.86: 50 107.86 - 143.81: 2 143.81 - 179.77: 9 Dihedral angle restraints: 14917 sinusoidal: 6886 harmonic: 8031 Sorted by residual: dihedral pdb=" C4' C I 31 " pdb=" C3' C I 31 " pdb=" C2' C I 31 " pdb=" C1' C I 31 " ideal model delta sinusoidal sigma weight residual -35.00 33.42 -68.42 1 8.00e+00 1.56e-02 9.48e+01 dihedral pdb=" C5' C I 31 " pdb=" C4' C I 31 " pdb=" C3' C I 31 " pdb=" O3' C I 31 " ideal model delta sinusoidal sigma weight residual 147.00 80.19 66.81 1 8.00e+00 1.56e-02 9.09e+01 dihedral pdb=" O4' C I 6 " pdb=" C1' C I 6 " pdb=" N1 C I 6 " pdb=" C2 C I 6 " ideal model delta sinusoidal sigma weight residual 200.00 49.79 150.21 1 1.50e+01 4.44e-03 7.97e+01 ... (remaining 14914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3668 0.121 - 0.242: 259 0.242 - 0.363: 18 0.363 - 0.484: 3 0.484 - 0.605: 6 Chirality restraints: 3954 Sorted by residual: chirality pdb=" CB VAL E 5 " pdb=" CA VAL E 5 " pdb=" CG1 VAL E 5 " pdb=" CG2 VAL E 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.16e+00 chirality pdb=" CB VAL F 194 " pdb=" CA VAL F 194 " pdb=" CG1 VAL F 194 " pdb=" CG2 VAL F 194 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.22e+00 chirality pdb=" CB ILE L 619 " pdb=" CA ILE L 619 " pdb=" CG1 ILE L 619 " pdb=" CG2 ILE L 619 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.55 2.00e-01 2.50e+01 7.48e+00 ... (remaining 3951 not shown) Planarity restraints: 4034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 612 " -0.043 2.00e-02 2.50e+03 3.68e-02 3.39e+01 pdb=" CG TRP L 612 " 0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP L 612 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TRP L 612 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP L 612 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP L 612 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP L 612 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 612 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 612 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP L 612 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 242 " 0.026 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C GLY D 242 " -0.092 2.00e-02 2.50e+03 pdb=" O GLY D 242 " 0.036 2.00e-02 2.50e+03 pdb=" N LEU D 243 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 212 " 0.032 2.00e-02 2.50e+03 3.14e-02 2.46e+01 pdb=" CG TRP H 212 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP H 212 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP H 212 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 212 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 212 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 212 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 212 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 212 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 212 " 0.003 2.00e-02 2.50e+03 ... (remaining 4031 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 62 2.29 - 2.94: 10570 2.94 - 3.60: 37497 3.60 - 4.25: 61748 4.25 - 4.90: 99029 Nonbonded interactions: 208906 Sorted by model distance: nonbonded pdb=" N4 C I 48 " pdb=" O6 G I 60 " model vdw 1.641 2.520 nonbonded pdb=" NH2 ARG L 557 " pdb=" OE2 GLU L 562 " model vdw 1.707 2.520 nonbonded pdb=" OG SER H 190 " pdb=" CD2 LEU H 192 " model vdw 1.731 3.460 nonbonded pdb=" O ILE F 185 " pdb=" CD2 LEU F 188 " model vdw 1.778 3.460 nonbonded pdb=" CB LYS D 244 " pdb=" O6 DG K 32 " model vdw 1.810 3.440 ... (remaining 208901 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 'C' and (resid 1 through 216 or resid 240 through 343)) selection = (chain 'D' and (resid 1 through 216 or resid 240 through 343)) selection = (chain 'E' and (resid 1 through 216 or resid 240 through 343)) selection = (chain 'F' and resid 1 through 343) } 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 10.510 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 75.160 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.090 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:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 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 : 0.007 0.270 25130 Z= 0.461 Angle : 1.123 13.990 34671 Z= 0.652 Chirality : 0.068 0.605 3954 Planarity : 0.009 0.115 4034 Dihedral : 20.099 179.768 9769 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.90 % Rotamer: Outliers : 1.26 % Allowed : 20.26 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.14), residues: 2803 helix: -1.66 (0.14), residues: 975 sheet: -1.08 (0.22), residues: 474 loop : -1.61 (0.15), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.004 TRP L 612 HIS 0.017 0.002 HIS L 141 PHE 0.071 0.003 PHE F 341 TYR 0.058 0.003 TYR A 217 ARG 0.019 0.001 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 402 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 5 residues processed: 421 average time/residue: 1.2509 time to fit residues: 618.0637 Evaluate side-chains 340 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 335 time to evaluate : 2.563 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 3 average time/residue: 0.6873 time to fit residues: 6.2123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 148 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 chunk 228 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 138 optimal weight: 0.0970 chunk 169 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 116 HIS ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 280 ASN ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN E 284 ASN F 2 GLN ** F 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 GLN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN ** H 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 GLN ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 283 GLN L 556 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25130 Z= 0.229 Angle : 0.712 12.038 34671 Z= 0.362 Chirality : 0.045 0.281 3954 Planarity : 0.006 0.071 4034 Dihedral : 19.993 178.820 4685 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.10 % Favored : 96.86 % Rotamer: Outliers : 4.48 % Allowed : 21.43 % Favored : 74.09 % 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: -1.46 (0.15), residues: 2803 helix: -0.46 (0.16), residues: 995 sheet: -0.97 (0.22), residues: 477 loop : -1.27 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 177 HIS 0.008 0.001 HIS L 141 PHE 0.018 0.001 PHE E 133 TYR 0.018 0.001 TYR C 47 ARG 0.011 0.001 ARG D 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 370 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 33 residues processed: 437 average time/residue: 1.1993 time to fit residues: 619.2704 Evaluate side-chains 350 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 317 time to evaluate : 2.631 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 19 residues processed: 14 average time/residue: 0.5002 time to fit residues: 13.3675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 219 optimal weight: 7.9990 chunk 179 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 264 optimal weight: 0.9990 chunk 285 optimal weight: 3.9990 chunk 235 optimal weight: 30.0000 chunk 262 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN E 92 ASN E 106 ASN E 155 ASN ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN F 2 GLN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 GLN ** L 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 450 GLN L 472 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25130 Z= 0.261 Angle : 0.692 9.822 34671 Z= 0.351 Chirality : 0.045 0.267 3954 Planarity : 0.005 0.060 4034 Dihedral : 19.837 179.974 4685 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.83 % Allowed : 21.04 % Favored : 73.13 % 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: -1.13 (0.15), residues: 2803 helix: 0.03 (0.16), residues: 991 sheet: -1.04 (0.22), residues: 466 loop : -1.16 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 177 HIS 0.008 0.001 HIS L 141 PHE 0.017 0.002 PHE E 133 TYR 0.017 0.002 TYR G 99 ARG 0.007 0.001 ARG G 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 351 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 51 residues processed: 442 average time/residue: 1.1347 time to fit residues: 596.8742 Evaluate side-chains 375 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 324 time to evaluate : 2.523 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 34 residues processed: 17 average time/residue: 0.5391 time to fit residues: 15.9885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 67.4259 > 50: distance: 31 - 36: 32.752 distance: 36 - 37: 27.583 distance: 37 - 38: 34.224 distance: 37 - 40: 20.303 distance: 38 - 39: 49.125 distance: 38 - 44: 12.989 distance: 40 - 41: 33.668 distance: 41 - 42: 36.129 distance: 41 - 43: 35.841 distance: 44 - 45: 55.030 distance: 45 - 46: 18.562 distance: 45 - 48: 23.831 distance: 46 - 47: 35.831 distance: 46 - 52: 43.478 distance: 48 - 49: 15.621 distance: 49 - 50: 19.655 distance: 49 - 51: 25.535 distance: 52 - 53: 47.182 distance: 52 - 58: 29.607 distance: 53 - 54: 67.426 distance: 53 - 56: 52.516 distance: 54 - 55: 52.458 distance: 54 - 59: 50.068 distance: 56 - 57: 20.384 distance: 57 - 58: 14.644 distance: 59 - 60: 10.662 distance: 60 - 61: 12.653 distance: 60 - 63: 16.705 distance: 61 - 62: 9.779 distance: 61 - 67: 21.120 distance: 63 - 64: 11.310 distance: 64 - 65: 6.711 distance: 64 - 66: 6.896 distance: 67 - 68: 10.209 distance: 68 - 69: 17.807 distance: 68 - 71: 8.322 distance: 69 - 70: 13.599 distance: 69 - 76: 29.679 distance: 70 - 165: 17.845 distance: 71 - 72: 13.194 distance: 72 - 73: 6.799 distance: 73 - 74: 3.929 distance: 76 - 77: 21.098 distance: 77 - 78: 17.078 distance: 77 - 80: 15.150 distance: 78 - 79: 20.063 distance: 78 - 87: 23.609 distance: 80 - 81: 25.375 distance: 81 - 82: 6.589 distance: 82 - 83: 7.729 distance: 84 - 85: 3.664 distance: 87 - 88: 9.776 distance: 87 - 151: 9.073 distance: 88 - 89: 12.749 distance: 88 - 91: 9.493 distance: 89 - 90: 10.881 distance: 89 - 99: 12.864 distance: 91 - 92: 6.259 distance: 92 - 93: 5.666 distance: 92 - 94: 4.027 distance: 93 - 95: 6.907 distance: 94 - 96: 4.409 distance: 95 - 97: 3.273 distance: 100 - 101: 3.203 distance: 100 - 103: 6.679 distance: 103 - 104: 7.670 distance: 109 - 110: 10.772 distance: 109 - 112: 4.353 distance: 110 - 111: 15.297 distance: 110 - 113: 14.891 distance: 113 - 114: 8.206 distance: 113 - 119: 8.578 distance: 114 - 115: 9.358 distance: 114 - 117: 16.853 distance: 115 - 116: 12.868 distance: 115 - 120: 10.588 distance: 117 - 118: 7.349 distance: 118 - 119: 11.651