Starting phenix.real_space_refine on Sat May 24 01:28:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v8o_21107/05_2025/6v8o_21107.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v8o_21107/05_2025/6v8o_21107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v8o_21107/05_2025/6v8o_21107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v8o_21107/05_2025/6v8o_21107.map" model { file = "/net/cci-nas-00/data/ceres_data/6v8o_21107/05_2025/6v8o_21107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v8o_21107/05_2025/6v8o_21107.cif" } resolution = 3.07 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= 0.005 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 1 6.06 5 S 91 5.16 5 C 15930 2.51 5 N 4277 2.21 5 O 4804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25103 Number of models: 1 Model: "" Number of chains: 23 Chain: "C" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 493 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "D" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 772 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain breaks: 1 Chain: "E" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 978 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "F" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 536 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 7, 'TRANS': 59} Chain breaks: 1 Chain: "G" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 422 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "H" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1083 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain breaks: 1 Chain: "I" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2416 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "J" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'TRANS': 114} Chain: "K" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 878 Classifications: {'peptide': 109} Link IDs: {'TRANS': 108} Chain breaks: 1 Chain: "L" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2445 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 2 Chain: "M" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2474 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 16, 'TRANS': 293} Chain breaks: 3 Chain: "N" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3275 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 18, 'TRANS': 393} Chain breaks: 1 Chain: "O" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3145 Classifications: {'peptide': 384} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 361} Chain breaks: 3 Chain: "Q" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2137 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 12, 'TRANS': 251} Chain breaks: 2 Chain: "R" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2126 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain breaks: 1 Chain: "S" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 278 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "2" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 28} Unresolved non-hydrogen planarities: 28 Chain: "3" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "4" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "5" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "6" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "7" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 245 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'UNK:plan-1': 49} Unresolved non-hydrogen planarities: 49 Chain: "I" 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 5813 SG CYS I 260 150.361 54.662 77.002 1.00 50.60 S ATOM 5836 SG CYS I 263 153.627 52.802 78.258 1.00 55.54 S ATOM 5999 SG CYS I 283 152.020 55.587 80.436 1.00 54.74 S ATOM 6022 SG CYS I 286 153.971 56.119 76.846 1.00 50.21 S Time building chain proxies: 13.27, per 1000 atoms: 0.53 Number of scatterers: 25103 At special positions: 0 Unit cell: (208.655, 130.949, 198.582, 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 1 29.99 S 91 16.00 O 4804 8.00 N 4277 7.00 C 15930 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 - 3.00 Amino acid : True - 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: 5.89 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 601 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 260 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 263 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 286 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 283 " Number of angles added : 6 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6118 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 17 sheets defined 56.4% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'C' and resid 20 through 40 Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 54 through 75 Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'D' and resid 27 through 35 Processing helix chain 'D' and resid 72 through 79 Processing helix chain 'D' and resid 93 through 99 Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.601A pdb=" N PHE D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 125 Processing helix chain 'E' and resid 318 through 343 Processing helix chain 'E' and resid 400 through 404 removed outlier: 4.236A pdb=" N SER E 403 " --> pdb=" O THR E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 411 removed outlier: 4.272A pdb=" N TYR E 410 " --> pdb=" O PRO E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 433 Processing helix chain 'F' and resid 862 through 867 Processing helix chain 'F' and resid 871 through 881 removed outlier: 3.765A pdb=" N MET F 881 " --> pdb=" O HIS F 877 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 196 removed outlier: 3.906A pdb=" N ILE G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 468 Processing helix chain 'I' and resid 58 through 72 Processing helix chain 'I' and resid 95 through 102 Processing helix chain 'I' and resid 103 through 106 Processing helix chain 'I' and resid 114 through 132 removed outlier: 3.756A pdb=" N SER I 132 " --> pdb=" O THR I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 146 removed outlier: 3.845A pdb=" N VAL I 142 " --> pdb=" O THR I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 163 removed outlier: 3.512A pdb=" N TRP I 163 " --> pdb=" O PHE I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 175 removed outlier: 4.099A pdb=" N LYS I 175 " --> pdb=" O PRO I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 244 Processing helix chain 'I' and resid 246 through 251 Processing helix chain 'I' and resid 283 through 289 Processing helix chain 'I' and resid 297 through 299 No H-bonds generated for 'chain 'I' and resid 297 through 299' Processing helix chain 'I' and resid 316 through 330 Processing helix chain 'I' and resid 333 through 342 removed outlier: 3.847A pdb=" N GLY I 342 " --> pdb=" O ALA I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 356 Processing helix chain 'I' and resid 360 through 368 Processing helix chain 'J' and resid 388 through 403 removed outlier: 3.624A pdb=" N CYS J 392 " --> pdb=" O LYS J 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 406 through 490 removed outlier: 3.834A pdb=" N VAL J 410 " --> pdb=" O LYS J 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 402 Processing helix chain 'K' and resid 421 through 489 Processing helix chain 'L' and resid 59 through 76 Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 96 through 102 Processing helix chain 'L' and resid 114 through 131 Processing helix chain 'L' and resid 138 through 145 removed outlier: 4.076A pdb=" N VAL L 142 " --> pdb=" O THR L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 163 Processing helix chain 'L' and resid 171 through 175 removed outlier: 3.541A pdb=" N LYS L 175 " --> pdb=" O PRO L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 292 Processing helix chain 'L' and resid 298 through 304 Processing helix chain 'L' and resid 316 through 330 Processing helix chain 'L' and resid 333 through 342 Processing helix chain 'L' and resid 346 through 356 Processing helix chain 'L' and resid 360 through 377 removed outlier: 3.583A pdb=" N ILE L 364 " --> pdb=" O GLU L 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 51 Processing helix chain 'M' and resid 237 through 242 removed outlier: 3.629A pdb=" N LEU M 241 " --> pdb=" O ASN M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 263 Processing helix chain 'M' and resid 268 through 275 Processing helix chain 'M' and resid 316 through 324 Processing helix chain 'M' and resid 331 through 342 removed outlier: 3.623A pdb=" N VAL M 335 " --> pdb=" O PRO M 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 372 through 377 Processing helix chain 'M' and resid 387 through 425 Processing helix chain 'M' and resid 425 through 445 Processing helix chain 'M' and resid 452 through 457 Processing helix chain 'M' and resid 470 through 472 No H-bonds generated for 'chain 'M' and resid 470 through 472' Processing helix chain 'M' and resid 473 through 480 Processing helix chain 'N' and resid 40 through 46 Processing helix chain 'N' and resid 65 through 70 removed outlier: 3.923A pdb=" N SER N 70 " --> pdb=" O VAL N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 92 removed outlier: 3.995A pdb=" N GLY N 92 " --> pdb=" O ALA N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 111 Processing helix chain 'N' and resid 123 through 140 removed outlier: 3.664A pdb=" N PHE N 127 " --> pdb=" O LEU N 123 " (cutoff:3.500A) Proline residue: N 133 - end of helix Processing helix chain 'N' and resid 148 through 170 Processing helix chain 'N' and resid 171 through 180 removed outlier: 3.691A pdb=" N LYS N 180 " --> pdb=" O GLN N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 201 Processing helix chain 'N' and resid 208 through 210 No H-bonds generated for 'chain 'N' and resid 208 through 210' Processing helix chain 'N' and resid 211 through 231 removed outlier: 3.878A pdb=" N SER N 231 " --> pdb=" O GLU N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 240 through 253 Processing helix chain 'N' and resid 255 through 269 removed outlier: 3.614A pdb=" N VAL N 259 " --> pdb=" O ASP N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 279 through 284 removed outlier: 3.521A pdb=" N ASP N 282 " --> pdb=" O SER N 279 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU N 284 " --> pdb=" O ALA N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 285 through 298 removed outlier: 3.565A pdb=" N LEU N 298 " --> pdb=" O SER N 294 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 317 Processing helix chain 'N' and resid 320 through 329 removed outlier: 4.334A pdb=" N SER N 329 " --> pdb=" O GLU N 325 " (cutoff:3.500A) Processing helix chain 'N' and resid 329 through 345 Proline residue: N 341 - end of helix removed outlier: 3.681A pdb=" N SER N 345 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 353 through 359 removed outlier: 3.800A pdb=" N GLN N 357 " --> pdb=" O TYR N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 524 through 539 removed outlier: 3.651A pdb=" N ASN N 539 " --> pdb=" O CYS N 535 " (cutoff:3.500A) Processing helix chain 'N' and resid 546 through 564 removed outlier: 3.749A pdb=" N CYS N 550 " --> pdb=" O GLY N 546 " (cutoff:3.500A) Proline residue: N 555 - end of helix Processing helix chain 'N' and resid 564 through 571 removed outlier: 3.513A pdb=" N THR N 568 " --> pdb=" O ILE N 564 " (cutoff:3.500A) Processing helix chain 'N' and resid 571 through 577 Processing helix chain 'O' and resid 10 through 25 Processing helix chain 'O' and resid 29 through 33 Processing helix chain 'O' and resid 43 through 45 No H-bonds generated for 'chain 'O' and resid 43 through 45' Processing helix chain 'O' and resid 46 through 61 Processing helix chain 'O' and resid 75 through 82 removed outlier: 3.518A pdb=" N ARG O 79 " --> pdb=" O THR O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 110 removed outlier: 3.500A pdb=" N PHE O 92 " --> pdb=" O ILE O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 138 removed outlier: 3.532A pdb=" N GLN O 118 " --> pdb=" O THR O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 179 Processing helix chain 'O' and resid 243 through 248 removed outlier: 4.029A pdb=" N VAL O 247 " --> pdb=" O ARG O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 302 through 314 Processing helix chain 'O' and resid 389 through 394 Processing helix chain 'O' and resid 403 through 412 removed outlier: 3.659A pdb=" N ILE O 407 " --> pdb=" O GLY O 403 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 436 removed outlier: 3.656A pdb=" N ASN O 436 " --> pdb=" O GLU O 432 " (cutoff:3.500A) Processing helix chain 'O' and resid 442 through 462 Processing helix chain 'Q' and resid 3 through 7 Processing helix chain 'Q' and resid 15 through 22 Processing helix chain 'Q' and resid 161 through 167 Processing helix chain 'Q' and resid 168 through 177 Processing helix chain 'Q' and resid 231 through 244 Processing helix chain 'Q' and resid 247 through 265 removed outlier: 3.553A pdb=" N LEU Q 265 " --> pdb=" O GLN Q 261 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 270 removed outlier: 3.629A pdb=" N ALA Q 270 " --> pdb=" O GLU Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 319 Processing helix chain 'Q' and resid 323 through 345 removed outlier: 4.018A pdb=" N LEU Q 327 " --> pdb=" O GLU Q 323 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER Q 329 " --> pdb=" O ILE Q 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 66 Processing helix chain 'R' and resid 68 through 73 Processing helix chain 'R' and resid 74 through 102 removed outlier: 3.502A pdb=" N ALA R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 127 Processing helix chain 'R' and resid 132 through 136 removed outlier: 4.081A pdb=" N LEU R 136 " --> pdb=" O ASP R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 172 removed outlier: 3.548A pdb=" N LEU R 172 " --> pdb=" O LYS R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 179 removed outlier: 4.106A pdb=" N PHE R 178 " --> pdb=" O GLU R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 208 Processing helix chain 'R' and resid 236 through 250 Processing helix chain 'R' and resid 250 through 267 Processing helix chain 'R' and resid 268 through 273 Processing helix chain 'R' and resid 273 through 278 Processing helix chain 'R' and resid 279 through 290 removed outlier: 3.635A pdb=" N GLN R 290 " --> pdb=" O GLN R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 318 Processing helix chain 'S' and resid 204 through 227 removed outlier: 3.744A pdb=" N GLN S 227 " --> pdb=" O LEU S 223 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 20 Processing helix chain '4' and resid 1 through 18 Processing helix chain '5' and resid 4 through 16 Processing helix chain '6' and resid 421 through 434 Processing sheet with id=AA1, first strand: chain 'E' and resid 349 through 351 removed outlier: 3.734A pdb=" N GLY L 180 " --> pdb=" O ILE E 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 368 through 373 removed outlier: 6.977A pdb=" N VAL E 368 " --> pdb=" O ASP I 192 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP I 192 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY E 370 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL E 385 " --> pdb=" O PHE I 187 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL I 189 " --> pdb=" O VAL E 385 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU E 387 " --> pdb=" O VAL I 189 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU I 191 " --> pdb=" O GLU E 387 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL E 389 " --> pdb=" O LEU I 191 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS I 231 " --> pdb=" O THR E 388 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE E 390 " --> pdb=" O THR I 229 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR I 229 " --> pdb=" O ILE E 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 157 through 160 removed outlier: 3.503A pdb=" N SER S 201 " --> pdb=" O ASN G 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 589 through 594 removed outlier: 4.072A pdb=" N HIS H 514 " --> pdb=" O GLN H 453 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLN H 453 " --> pdb=" O HIS H 514 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER H 458 " --> pdb=" O VAL H 482 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL H 482 " --> pdb=" O SER H 458 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP H 481 " --> pdb=" O ILE L 259 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N HIS L 261 " --> pdb=" O TRP H 481 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU H 483 " --> pdb=" O HIS L 261 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR L 262 " --> pdb=" O ASN L 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 522 through 526 removed outlier: 6.052A pdb=" N PHE H 498 " --> pdb=" O TRP H 620 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ASN H 622 " --> pdb=" O PHE H 498 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE H 500 " --> pdb=" O ASN H 622 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA H 497 " --> pdb=" O ILE O 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 80 through 83 Processing sheet with id=AA7, first strand: chain 'I' and resid 256 through 257 removed outlier: 3.664A pdb=" N VAL N 47 " --> pdb=" O VAL I 257 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 281 through 282 Processing sheet with id=AA9, first strand: chain 'K' and resid 493 through 497 Processing sheet with id=AB1, first strand: chain 'M' and resid 368 through 369 removed outlier: 3.543A pdb=" N LEU M 368 " --> pdb=" O ILE M 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG M 75 " --> pdb=" O UNK 7 24 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR M 77 " --> pdb=" O UNK 7 26 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR M 79 " --> pdb=" O UNK 7 28 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 349 through 352 removed outlier: 6.582A pdb=" N SER M 219 " --> pdb=" O UNK 7 62 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N UNK 7 64 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR M 221 " --> pdb=" O UNK 7 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 246 through 247 Processing sheet with id=AB4, first strand: chain 'M' and resid 313 through 314 removed outlier: 3.531A pdb=" N LEU M 330 " --> pdb=" O VAL M 313 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 476 through 477 Processing sheet with id=AB6, first strand: chain 'Q' and resid 13 through 14 removed outlier: 3.566A pdb=" N LYS Q 179 " --> pdb=" O SER Q 14 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 203 through 212 Processing sheet with id=AB8, first strand: chain 'Q' and resid 278 through 286 1297 hydrogen bonds defined for protein. 3765 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: 7.21 Time building geometry restraints manager: 6.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8274 1.34 - 1.46: 4234 1.46 - 1.57: 12890 1.57 - 1.69: 0 1.69 - 1.81: 145 Bond restraints: 25543 Sorted by residual: bond pdb=" CB TRP I 163 " pdb=" CG TRP I 163 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.30e+00 bond pdb=" CA LEU N 132 " pdb=" C LEU N 132 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.26e-02 6.30e+03 1.20e+00 bond pdb=" C TYR O 85 " pdb=" N GLU O 86 " ideal model delta sigma weight residual 1.329 1.297 0.031 3.03e-02 1.09e+03 1.08e+00 bond pdb=" C LEU N 132 " pdb=" O LEU N 132 " ideal model delta sigma weight residual 1.238 1.251 -0.013 1.28e-02 6.10e+03 1.07e+00 bond pdb=" C PHE R 135 " pdb=" N LEU R 136 " ideal model delta sigma weight residual 1.332 1.318 0.014 1.40e-02 5.10e+03 9.94e-01 ... (remaining 25538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 34433 2.96 - 5.92: 112 5.92 - 8.87: 8 8.87 - 11.83: 1 11.83 - 14.79: 1 Bond angle restraints: 34555 Sorted by residual: angle pdb=" N SER Q 374 " pdb=" CA SER Q 374 " pdb=" C SER Q 374 " ideal model delta sigma weight residual 110.80 120.59 -9.79 2.13e+00 2.20e-01 2.11e+01 angle pdb=" C ILE H 528 " pdb=" N ASN H 529 " pdb=" CA ASN H 529 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C GLY Q 373 " pdb=" N SER Q 374 " pdb=" CA SER Q 374 " ideal model delta sigma weight residual 121.54 129.11 -7.57 1.91e+00 2.74e-01 1.57e+01 angle pdb=" N PRO O 415 " pdb=" CA PRO O 415 " pdb=" C PRO O 415 " ideal model delta sigma weight residual 114.18 110.44 3.74 1.39e+00 5.18e-01 7.23e+00 angle pdb=" C SER Q 374 " pdb=" CA SER Q 374 " pdb=" CB SER Q 374 " ideal model delta sigma weight residual 110.42 105.22 5.20 1.99e+00 2.53e-01 6.84e+00 ... (remaining 34550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 14796 17.77 - 35.54: 707 35.54 - 53.31: 140 53.31 - 71.09: 34 71.09 - 88.86: 6 Dihedral angle restraints: 15683 sinusoidal: 6343 harmonic: 9340 Sorted by residual: dihedral pdb=" CA GLU Q 371 " pdb=" C GLU Q 371 " pdb=" N LEU Q 372 " pdb=" CA LEU Q 372 " ideal model delta harmonic sigma weight residual -180.00 -153.93 -26.07 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ASN H 529 " pdb=" C ASN H 529 " pdb=" N LYS H 530 " pdb=" CA LYS H 530 " ideal model delta harmonic sigma weight residual 180.00 155.34 24.66 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLY Q 373 " pdb=" C GLY Q 373 " pdb=" N SER Q 374 " pdb=" CA SER Q 374 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 15680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2642 0.033 - 0.066: 973 0.066 - 0.099: 233 0.099 - 0.133: 118 0.133 - 0.166: 5 Chirality restraints: 3971 Sorted by residual: chirality pdb=" CA ILE E 359 " pdb=" N ILE E 359 " pdb=" C ILE E 359 " pdb=" CB ILE E 359 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ILE N 514 " pdb=" N ILE N 514 " pdb=" C ILE N 514 " pdb=" CB ILE N 514 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA SER Q 374 " pdb=" N SER Q 374 " pdb=" C SER Q 374 " pdb=" CB SER Q 374 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 3968 not shown) Planarity restraints: 4440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE N 564 " -0.048 5.00e-02 4.00e+02 7.37e-02 8.70e+00 pdb=" N PRO N 565 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO N 565 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO N 565 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN M 6 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO M 7 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO M 7 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO M 7 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU N 124 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO N 125 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO N 125 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO N 125 " -0.025 5.00e-02 4.00e+02 ... (remaining 4437 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 668 2.70 - 3.25: 25129 3.25 - 3.80: 37366 3.80 - 4.35: 48918 4.35 - 4.90: 82429 Nonbonded interactions: 194510 Sorted by model distance: nonbonded pdb=" O GLU N 227 " pdb=" OG SER N 230 " model vdw 2.149 3.040 nonbonded pdb=" OH TYR Q 184 " pdb=" OD1 ASP Q 242 " model vdw 2.150 3.040 nonbonded pdb=" OE2 GLU O 41 " pdb=" OG SER O 50 " model vdw 2.163 3.040 nonbonded pdb=" O LYS H 449 " pdb=" OG1 THR H 516 " model vdw 2.164 3.040 nonbonded pdb=" OD1 ASN Q 282 " pdb=" ND2 ASN Q 295 " model vdw 2.201 3.120 ... (remaining 194505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '3' selection = chain '4' } ncs_group { reference = chain '5' selection = (chain '6' and resid 421 through 434) } ncs_group { reference = (chain 'I' and (resid 58 through 304 or resid 312 through 368)) selection = (chain 'L' and (resid 58 through 202 or resid 222 through 368)) } ncs_group { reference = (chain 'J' and (resid 387 through 402 or resid 420 through 501)) selection = (chain 'K' and resid 387 through 501) } 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: 1.070 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: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 54.040 Find NCS groups from input model: 0.570 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 : 0.004 0.068 25547 Z= 0.189 Angle : 0.554 14.790 34561 Z= 0.299 Chirality : 0.039 0.166 3971 Planarity : 0.003 0.074 4440 Dihedral : 11.206 88.857 9565 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.89 % Favored : 93.01 % Rotamer: Outliers : 2.31 % Allowed : 5.62 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -1.57 (0.14), residues: 2946 helix: 0.34 (0.13), residues: 1511 sheet: -0.89 (0.36), residues: 187 loop : -2.91 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP O 273 HIS 0.004 0.001 HIS N 220 PHE 0.012 0.001 PHE I 85 TYR 0.015 0.001 TYR I 272 ARG 0.003 0.000 ARG Q 19 Details of bonding type rmsd hydrogen bonds : bond 0.13786 ( 1297) hydrogen bonds : angle 5.58856 ( 3765) metal coordination : bond 0.06372 ( 4) metal coordination : angle 6.00010 ( 6) covalent geometry : bond 0.00417 (25543) covalent geometry : angle 0.54855 (34555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 682 time to evaluate : 2.952 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: C 48 ARG cc_start: 0.7326 (ttt90) cc_final: 0.7065 (tmt170) REVERT: D 94 ARG cc_start: 0.6705 (ttt180) cc_final: 0.6372 (ttt-90) REVERT: D 107 HIS cc_start: 0.7234 (t70) cc_final: 0.6968 (t-90) REVERT: E 329 ARG cc_start: 0.7079 (mtm110) cc_final: 0.6539 (mmt180) REVERT: E 353 TYR cc_start: 0.8604 (m-80) cc_final: 0.8031 (m-80) REVERT: E 430 LYS cc_start: 0.8227 (mttt) cc_final: 0.8021 (mtmt) REVERT: F 817 ARG cc_start: 0.6858 (mtp180) cc_final: 0.6477 (mtp85) REVERT: G 167 MET cc_start: 0.8383 (ttm) cc_final: 0.7454 (mtp) REVERT: G 189 LEU cc_start: 0.7023 (mt) cc_final: 0.6772 (mt) REVERT: I 191 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7780 (pp) REVERT: I 255 HIS cc_start: 0.6476 (p-80) cc_final: 0.6193 (m170) REVERT: I 281 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8570 (m-40) REVERT: J 388 LYS cc_start: 0.7808 (mttt) cc_final: 0.7329 (mppt) REVERT: J 390 MET cc_start: 0.7978 (mmm) cc_final: 0.7726 (mmm) REVERT: J 394 ASN cc_start: 0.8741 (m-40) cc_final: 0.8443 (m110) REVERT: J 437 MET cc_start: 0.7769 (mmm) cc_final: 0.7245 (mmt) REVERT: K 475 LEU cc_start: 0.7844 (tp) cc_final: 0.7631 (mm) REVERT: K 485 SER cc_start: 0.7064 (t) cc_final: 0.6522 (p) REVERT: K 501 GLN cc_start: 0.6941 (mt0) cc_final: 0.6576 (mt0) REVERT: K 503 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.5326 (m-30) REVERT: L 317 ASP cc_start: 0.7461 (m-30) cc_final: 0.7225 (m-30) REVERT: M 40 ASP cc_start: 0.8293 (t70) cc_final: 0.8087 (t70) REVERT: M 391 THR cc_start: 0.6244 (m) cc_final: 0.5833 (p) REVERT: N 85 MET cc_start: 0.8801 (mtm) cc_final: 0.8126 (mtm) REVERT: N 102 LYS cc_start: 0.8000 (mttt) cc_final: 0.7671 (mtpp) REVERT: N 104 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.6830 (m-10) REVERT: N 170 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8454 (mp10) REVERT: N 293 VAL cc_start: 0.8319 (t) cc_final: 0.8014 (t) REVERT: N 329 SER cc_start: 0.8300 (t) cc_final: 0.7858 (m) REVERT: N 551 GLN cc_start: 0.8485 (mt0) cc_final: 0.8272 (mt0) REVERT: N 553 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8393 (tt) REVERT: O 122 LYS cc_start: 0.6902 (tttt) cc_final: 0.6296 (tmtt) REVERT: Q 173 ASP cc_start: 0.6972 (m-30) cc_final: 0.6599 (t0) REVERT: Q 203 MET cc_start: 0.8732 (mmt) cc_final: 0.8357 (mmt) REVERT: Q 266 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7333 (pt0) REVERT: Q 294 ASP cc_start: 0.7805 (t0) cc_final: 0.7351 (t0) REVERT: Q 303 LYS cc_start: 0.8529 (mttt) cc_final: 0.8305 (mmtt) REVERT: R 193 ILE cc_start: 0.8099 (mt) cc_final: 0.7825 (pt) REVERT: R 306 GLU cc_start: 0.6363 (mt-10) cc_final: 0.6040 (pt0) REVERT: S 218 ASN cc_start: 0.6751 (m-40) cc_final: 0.6270 (t0) outliers start: 64 outliers final: 16 residues processed: 729 average time/residue: 0.3850 time to fit residues: 425.7234 Evaluate side-chains 407 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 385 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 281 ASN Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain K residue 503 ASP Chi-restraints excluded: chain M residue 316 ASP Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 170 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain Q residue 342 ASP Chi-restraints excluded: chain Q residue 345 ASP Chi-restraints excluded: chain Q residue 368 ASP Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.0980 chunk 231 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 239 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 277 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 HIS D 64 HIS D 108 HIS D 122 HIS E 331 ASN E 425 GLN E 432 ASN F 816 ASN F 855 ASN H 452 GLN H 494 ASN H 506 GLN H 514 HIS H 529 ASN H 601 HIS I 167 ASN I 253 GLN I 314 ASN J 430 GLN K 430 GLN K 501 GLN L 145 ASN ** L 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 318 GLN M 340 ASN M 378 GLN M 380 GLN N 43 GLN N 69 GLN N 286 HIS N 512 ASN N 559 HIS O 18 GLN O 22 ASN O 97 HIS O 193 GLN O 482 ASN O 484 ASN Q 5 ASN ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 158 GLN Q 164 ASN Q 220 GLN Q 261 GLN Q 352 HIS R 116 ASN R 123 GLN R 204 ASN R 270 HIS R 290 GLN S 227 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.161246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.118109 restraints weight = 36307.864| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.61 r_work: 0.3248 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25547 Z= 0.136 Angle : 0.563 14.684 34561 Z= 0.288 Chirality : 0.040 0.233 3971 Planarity : 0.004 0.073 4440 Dihedral : 5.308 59.953 3399 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 2.63 % Allowed : 11.06 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -0.13 (0.15), residues: 2946 helix: 1.59 (0.13), residues: 1529 sheet: -0.55 (0.35), residues: 196 loop : -2.33 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 273 HIS 0.009 0.001 HIS N 220 PHE 0.031 0.001 PHE R 83 TYR 0.019 0.001 TYR O 178 ARG 0.006 0.000 ARG O 137 Details of bonding type rmsd hydrogen bonds : bond 0.05368 ( 1297) hydrogen bonds : angle 4.17156 ( 3765) metal coordination : bond 0.00591 ( 4) metal coordination : angle 3.72563 ( 6) covalent geometry : bond 0.00292 (25543) covalent geometry : angle 0.56125 (34555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 410 time to evaluate : 3.102 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: C 48 ARG cc_start: 0.7429 (ttt90) cc_final: 0.7143 (tmt170) REVERT: D 94 ARG cc_start: 0.7076 (ttt180) cc_final: 0.6652 (ttt-90) REVERT: D 107 HIS cc_start: 0.7538 (t70) cc_final: 0.7207 (t-90) REVERT: E 329 ARG cc_start: 0.7683 (mtm110) cc_final: 0.6554 (mmt180) REVERT: E 407 LYS cc_start: 0.7226 (pttp) cc_final: 0.6921 (ptmm) REVERT: F 817 ARG cc_start: 0.7095 (mtp180) cc_final: 0.6256 (mtp85) REVERT: G 167 MET cc_start: 0.8320 (ttm) cc_final: 0.7543 (mtp) REVERT: H 589 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7292 (mt-10) REVERT: H 613 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6881 (mt-10) REVERT: I 312 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7527 (tptt) REVERT: I 317 ASP cc_start: 0.8133 (m-30) cc_final: 0.7839 (m-30) REVERT: J 388 LYS cc_start: 0.7918 (mttt) cc_final: 0.7529 (mppt) REVERT: J 390 MET cc_start: 0.8110 (mmm) cc_final: 0.7811 (mmm) REVERT: J 395 ASP cc_start: 0.8687 (m-30) cc_final: 0.8407 (m-30) REVERT: J 437 MET cc_start: 0.8554 (mmm) cc_final: 0.7951 (mmt) REVERT: J 463 LYS cc_start: 0.8087 (mmmt) cc_final: 0.7594 (mmmt) REVERT: L 81 ILE cc_start: 0.8656 (mp) cc_final: 0.8453 (mp) REVERT: L 149 ASP cc_start: 0.7860 (p0) cc_final: 0.7515 (p0) REVERT: L 239 GLN cc_start: 0.8782 (mt0) cc_final: 0.8569 (mt0) REVERT: L 312 LYS cc_start: 0.7230 (mttt) cc_final: 0.6425 (tptt) REVERT: L 317 ASP cc_start: 0.8577 (m-30) cc_final: 0.8190 (m-30) REVERT: N 69 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7961 (mm110) REVERT: N 102 LYS cc_start: 0.8868 (mttt) cc_final: 0.8534 (mtpp) REVERT: N 104 TYR cc_start: 0.9262 (OUTLIER) cc_final: 0.7524 (m-80) REVERT: N 170 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8629 (mp10) REVERT: N 293 VAL cc_start: 0.8342 (t) cc_final: 0.8083 (t) REVERT: N 521 GLN cc_start: 0.8129 (pm20) cc_final: 0.7844 (mp10) REVERT: N 522 GLU cc_start: 0.8451 (pt0) cc_final: 0.8247 (pm20) REVERT: N 551 GLN cc_start: 0.8840 (mt0) cc_final: 0.8616 (mt0) REVERT: N 553 ILE cc_start: 0.8548 (tt) cc_final: 0.8090 (tp) REVERT: O 122 LYS cc_start: 0.6884 (tttt) cc_final: 0.6073 (tmtt) REVERT: O 137 ARG cc_start: 0.6910 (ttm-80) cc_final: 0.6577 (ttt180) REVERT: O 196 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8245 (tt0) REVERT: O 215 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6844 (t0) REVERT: O 265 MET cc_start: 0.8526 (mtt) cc_final: 0.7940 (mtt) REVERT: Q 173 ASP cc_start: 0.7827 (m-30) cc_final: 0.7324 (t0) REVERT: Q 266 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7533 (pt0) REVERT: Q 303 LYS cc_start: 0.8617 (mttt) cc_final: 0.8215 (mmtt) REVERT: R 97 LEU cc_start: 0.7709 (tt) cc_final: 0.7387 (tp) REVERT: R 101 ARG cc_start: 0.7581 (ttm-80) cc_final: 0.7310 (mtt90) REVERT: R 221 CYS cc_start: 0.8846 (m) cc_final: 0.8449 (p) REVERT: R 234 MET cc_start: 0.8932 (mmm) cc_final: 0.7553 (mmm) REVERT: R 306 GLU cc_start: 0.6294 (mt-10) cc_final: 0.5888 (pt0) REVERT: S 218 ASN cc_start: 0.6691 (m-40) cc_final: 0.6243 (t0) outliers start: 73 outliers final: 42 residues processed: 458 average time/residue: 0.3775 time to fit residues: 269.5273 Evaluate side-chains 392 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 346 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 237 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 244 MET Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 170 GLN Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 321 GLN Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 215 ASP Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 264 MET Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 406 GLU Chi-restraints excluded: chain Q residue 268 ILE Chi-restraints excluded: chain Q residue 376 TRP Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain S residue 213 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.9096 > 50: distance: 122 - 128: 25.748 distance: 128 - 129: 36.710 distance: 129 - 130: 31.845 distance: 129 - 132: 42.517 distance: 130 - 131: 46.444 distance: 130 - 136: 47.457 distance: 132 - 133: 57.689 distance: 133 - 134: 39.698 distance: 133 - 135: 49.298 distance: 136 - 137: 34.662 distance: 137 - 138: 40.122 distance: 137 - 140: 37.135 distance: 138 - 139: 45.940 distance: 138 - 148: 42.627 distance: 140 - 141: 22.094 distance: 141 - 142: 6.900 distance: 141 - 143: 4.979 distance: 142 - 144: 12.742 distance: 143 - 145: 19.786 distance: 144 - 146: 19.957 distance: 145 - 146: 14.620 distance: 146 - 147: 16.343 distance: 148 - 149: 26.716 distance: 149 - 150: 21.118 distance: 149 - 152: 27.609 distance: 150 - 151: 20.964 distance: 150 - 157: 15.588 distance: 152 - 153: 10.274 distance: 153 - 154: 10.519 distance: 154 - 155: 3.145 distance: 154 - 156: 3.342 distance: 157 - 158: 23.866 distance: 158 - 159: 45.057 distance: 158 - 161: 34.529 distance: 159 - 160: 52.056 distance: 159 - 165: 32.320 distance: 161 - 162: 28.025 distance: 161 - 163: 19.864 distance: 162 - 164: 15.227 distance: 165 - 166: 16.512 distance: 166 - 167: 37.881 distance: 166 - 169: 24.529 distance: 167 - 168: 36.847 distance: 167 - 173: 52.786 distance: 168 - 191: 39.448 distance: 169 - 170: 11.022 distance: 170 - 171: 14.799 distance: 170 - 172: 5.521 distance: 173 - 174: 36.362 distance: 173 - 179: 46.585 distance: 174 - 175: 10.241 distance: 174 - 177: 27.270 distance: 175 - 176: 16.338 distance: 175 - 180: 9.677 distance: 177 - 178: 17.420 distance: 178 - 179: 19.625 distance: 180 - 181: 15.913 distance: 181 - 182: 7.264 distance: 181 - 184: 11.950 distance: 182 - 183: 19.148 distance: 182 - 191: 17.530 distance: 184 - 185: 8.245 distance: 185 - 186: 11.525 distance: 191 - 192: 34.894 distance: 192 - 193: 22.045 distance: 192 - 195: 34.563 distance: 193 - 194: 24.694 distance: 193 - 198: 9.049 distance: 195 - 196: 43.492 distance: 195 - 197: 30.326 distance: 198 - 199: 8.017 distance: 199 - 200: 21.859 distance: 199 - 202: 14.842 distance: 200 - 201: 32.465 distance: 200 - 207: 38.365 distance: 202 - 203: 20.247 distance: 203 - 204: 7.618 distance: 204 - 205: 6.131 distance: 205 - 206: 8.412 distance: 207 - 208: 17.582 distance: 207 - 213: 19.584 distance: 208 - 209: 6.395 distance: 208 - 211: 4.036 distance: 209 - 210: 16.504 distance: 209 - 214: 8.246 distance: 211 - 212: 14.298 distance: 212 - 213: 9.331