Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 12 02:56:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6igm_9668/10_2023/6igm_9668.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6igm_9668/10_2023/6igm_9668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6igm_9668/10_2023/6igm_9668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6igm_9668/10_2023/6igm_9668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6igm_9668/10_2023/6igm_9668.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6igm_9668/10_2023/6igm_9668.pdb" } resolution = 4.0 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= 0.005 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: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 15295 2.51 5 N 4225 2.21 5 O 4622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B ARG 438": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 276": "NH1" <-> "NH2" Residue "C ARG 333": "NH1" <-> "NH2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D GLU 285": "OE1" <-> "OE2" Residue "D GLU 286": "OE1" <-> "OE2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D ARG 374": "NH1" <-> "NH2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D ARG 428": "NH1" <-> "NH2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E ARG 118": "NH1" <-> "NH2" Residue "E ARG 276": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ARG 362": "NH1" <-> "NH2" Residue "E ARG 378": "NH1" <-> "NH2" Residue "E ARG 404": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 21": "NH1" <-> "NH2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 314": "NH1" <-> "NH2" Residue "F ARG 353": "NH1" <-> "NH2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F ARG 400": "NH1" <-> "NH2" Residue "F ARG 438": "NH1" <-> "NH2" Residue "G ARG 31": "NH1" <-> "NH2" Residue "G ARG 36": "NH1" <-> "NH2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G ARG 124": "NH1" <-> "NH2" Residue "G ARG 134": "NH1" <-> "NH2" Residue "G ARG 137": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 172": "NH1" <-> "NH2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 274": "NH1" <-> "NH2" Residue "G ARG 330": "NH1" <-> "NH2" Residue "G ARG 332": "NH1" <-> "NH2" Residue "G ARG 338": "NH1" <-> "NH2" Residue "G ARG 379": "NH1" <-> "NH2" Residue "H ARG 945": "NH1" <-> "NH2" Residue "H GLU 952": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 24257 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3123 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 15, 'TRANS': 389} Chain breaks: 2 Chain: "B" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3090 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 3 Chain: "C" Number of atoms: 2852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2852 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain breaks: 5 Chain: "D" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3078 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 9, 'TRANS': 386} Chain breaks: 3 Chain: "E" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2935 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 15, 'TRANS': 364} Chain breaks: 3 Chain: "F" Number of atoms: 2852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2852 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 8, 'TRANS': 357} Chain breaks: 4 Chain: "G" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2987 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 15, 'TRANS': 350} Chain breaks: 1 Chain: "H" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3030 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 26, 'TRANS': 346} Chain breaks: 4 Chain: "X" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 310 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'TRANS': 61} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'UNK:plan-1': 62} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 11.97, per 1000 atoms: 0.49 Number of scatterers: 24257 At special positions: 0 Unit cell: (162, 167.4, 139.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 4622 8.00 N 4225 7.00 C 15295 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.42 Conformation dependent library (CDL) restraints added in 3.4 seconds 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5818 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 28 sheets defined 42.8% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 42 through 58 removed outlier: 3.620A pdb=" N ILE A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.584A pdb=" N LEU A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.602A pdb=" N ILE A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 183 removed outlier: 4.094A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.556A pdb=" N ARG A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 289 removed outlier: 3.551A pdb=" N GLU A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.996A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.507A pdb=" N ASP A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 383 Processing helix chain 'A' and resid 388 through 401 removed outlier: 3.663A pdb=" N THR A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 421 removed outlier: 3.979A pdb=" N SER A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.807A pdb=" N VAL A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'B' and resid 49 through 66 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.735A pdb=" N ILE B 86 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 removed outlier: 3.560A pdb=" N ILE B 127 " --> pdb=" O PHE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.797A pdb=" N ILE B 179 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU B 180 " --> pdb=" O LYS B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 180' Processing helix chain 'B' and resid 245 through 252 removed outlier: 3.689A pdb=" N VAL B 249 " --> pdb=" O HIS B 245 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 260 removed outlier: 3.648A pdb=" N LEU B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 305 through 316 removed outlier: 3.755A pdb=" N ARG B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.851A pdb=" N GLY B 345 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 346 " --> pdb=" O PRO B 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 342 through 346' Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 363 through 378 removed outlier: 3.520A pdb=" N GLN B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 398 through 417 removed outlier: 3.537A pdb=" N ALA B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 433 removed outlier: 3.830A pdb=" N ILE B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 444 removed outlier: 4.003A pdb=" N LYS B 444 " --> pdb=" O GLN B 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 4.261A pdb=" N VAL C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 88 Processing helix chain 'C' and resid 110 through 120 removed outlier: 4.238A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 277 through 288 Processing helix chain 'C' and resid 308 through 320 removed outlier: 3.524A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 367 through 383 Processing helix chain 'C' and resid 387 through 401 Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.501A pdb=" N SER C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 421 Processing helix chain 'C' and resid 426 through 437 removed outlier: 3.748A pdb=" N VAL C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 446 Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.890A pdb=" N GLY D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 93 Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.928A pdb=" N SER D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 185 removed outlier: 3.929A pdb=" N ASP D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 Processing helix chain 'D' and resid 271 through 286 removed outlier: 3.898A pdb=" N GLN D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.558A pdb=" N MET D 303 " --> pdb=" O GLU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.766A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 354 removed outlier: 3.598A pdb=" N ARG D 353 " --> pdb=" O ASP D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 378 removed outlier: 3.502A pdb=" N GLU D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 397 removed outlier: 3.809A pdb=" N GLU D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 417 Processing helix chain 'D' and resid 422 through 433 removed outlier: 3.528A pdb=" N PHE D 433 " --> pdb=" O VAL D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 442 Processing helix chain 'E' and resid 42 through 59 removed outlier: 4.106A pdb=" N ILE E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL E 53 " --> pdb=" O CYS E 49 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU E 55 " --> pdb=" O VAL E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 86 removed outlier: 3.605A pdb=" N LEU E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 102 removed outlier: 3.840A pdb=" N VAL E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.789A pdb=" N VAL E 111 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 183 removed outlier: 3.539A pdb=" N PHE E 177 " --> pdb=" O ASP E 173 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 249 Processing helix chain 'E' and resid 271 through 288 removed outlier: 3.676A pdb=" N LEU E 275 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP E 288 " --> pdb=" O ASN E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 319 Processing helix chain 'E' and resid 346 through 350 removed outlier: 3.632A pdb=" N GLY E 349 " --> pdb=" O SER E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 356 removed outlier: 3.517A pdb=" N LEU E 355 " --> pdb=" O PRO E 351 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP E 356 " --> pdb=" O LEU E 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 351 through 356' Processing helix chain 'E' and resid 367 through 369 No H-bonds generated for 'chain 'E' and resid 367 through 369' Processing helix chain 'E' and resid 370 through 383 removed outlier: 4.065A pdb=" N ILE E 377 " --> pdb=" O GLN E 373 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG E 378 " --> pdb=" O ILE E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 401 Processing helix chain 'E' and resid 402 through 409 removed outlier: 3.863A pdb=" N SER E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 409 " --> pdb=" O TYR E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 421 removed outlier: 3.536A pdb=" N ASN E 414 " --> pdb=" O LEU E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 437 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.527A pdb=" N ILE F 86 " --> pdb=" O GLY F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 125 Processing helix chain 'F' and resid 245 through 252 removed outlier: 3.680A pdb=" N ASN F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER F 252 " --> pdb=" O ASP F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 286 removed outlier: 4.237A pdb=" N GLN F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE F 276 " --> pdb=" O VAL F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.697A pdb=" N PHE F 309 " --> pdb=" O ASP F 305 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 346 removed outlier: 3.627A pdb=" N GLY F 345 " --> pdb=" O SER F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 354 removed outlier: 3.985A pdb=" N LEU F 354 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 375 Processing helix chain 'F' and resid 385 through 397 removed outlier: 4.137A pdb=" N VAL F 389 " --> pdb=" O ASP F 385 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU F 396 " --> pdb=" O ARG F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 417 removed outlier: 3.633A pdb=" N ALA F 402 " --> pdb=" O SER F 398 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU F 411 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 removed outlier: 3.631A pdb=" N ILE F 426 " --> pdb=" O GLN F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 440 Processing helix chain 'G' and resid 68 through 80 removed outlier: 3.918A pdb=" N GLY G 80 " --> pdb=" O ASP G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 116 removed outlier: 3.546A pdb=" N GLN G 106 " --> pdb=" O PHE G 102 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU G 107 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU G 116 " --> pdb=" O ILE G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 135 removed outlier: 3.888A pdb=" N LEU G 130 " --> pdb=" O ASN G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 191 Processing helix chain 'G' and resid 200 through 209 Processing helix chain 'G' and resid 216 through 223 Processing helix chain 'G' and resid 271 through 275 removed outlier: 4.243A pdb=" N ARG G 274 " --> pdb=" O ALA G 271 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE G 275 " --> pdb=" O ASN G 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 271 through 275' Processing helix chain 'G' and resid 277 through 283 removed outlier: 4.287A pdb=" N LEU G 281 " --> pdb=" O VAL G 277 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE G 282 " --> pdb=" O PRO G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 287 Processing helix chain 'G' and resid 296 through 302 Processing helix chain 'G' and resid 304 through 308 Processing helix chain 'G' and resid 309 through 315 removed outlier: 3.707A pdb=" N LYS G 315 " --> pdb=" O PRO G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 326 removed outlier: 4.132A pdb=" N PHE G 326 " --> pdb=" O ASN G 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 323 through 326' Processing helix chain 'G' and resid 328 through 339 removed outlier: 3.958A pdb=" N ARG G 332 " --> pdb=" O GLY G 328 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS G 339 " --> pdb=" O SER G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 367 Processing helix chain 'G' and resid 378 through 382 Processing helix chain 'H' and resid 862 through 873 removed outlier: 3.853A pdb=" N MET H 873 " --> pdb=" O TYR H 869 " (cutoff:3.500A) Processing helix chain 'H' and resid 894 through 901 removed outlier: 3.877A pdb=" N ARG H 898 " --> pdb=" O LEU H 894 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS H 899 " --> pdb=" O MET H 895 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL H 900 " --> pdb=" O GLN H 896 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS H 901 " --> pdb=" O LEU H 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 894 through 901' Processing helix chain 'H' and resid 954 through 974 Proline residue: H 965 - end of helix Processing helix chain 'H' and resid 1901 through 1928 Proline residue: H1916 - end of helix Processing helix chain 'H' and resid 2004 through 2015 removed outlier: 4.447A pdb=" N LEU H2010 " --> pdb=" O PHE H2006 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA H2011 " --> pdb=" O GLN H2007 " (cutoff:3.500A) Processing helix chain 'H' and resid 2016 through 2018 No H-bonds generated for 'chain 'H' and resid 2016 through 2018' Processing helix chain 'H' and resid 2036 through 2042 removed outlier: 3.684A pdb=" N TYR H2040 " --> pdb=" O ARG H2036 " (cutoff:3.500A) Processing helix chain 'H' and resid 2042 through 2056 Processing helix chain 'H' and resid 2068 through 2080 removed outlier: 3.964A pdb=" N THR H2080 " --> pdb=" O GLU H2076 " (cutoff:3.500A) Processing helix chain 'H' and resid 2094 through 2103 Processing helix chain 'H' and resid 2144 through 2153 removed outlier: 3.693A pdb=" N ALA H2148 " --> pdb=" O MET H2144 " (cutoff:3.500A) Processing helix chain 'H' and resid 2172 through 2190 Processing helix chain 'X' and resid 53 through 62 removed outlier: 4.333A pdb=" N UNK X 59 " --> pdb=" O UNK X 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 97 removed outlier: 3.914A pdb=" N CYS A 94 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 300 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 299 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ALA A 330 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A 301 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.889A pdb=" N GLY A 121 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 157 through 163 Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 193 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 337 removed outlier: 3.988A pdb=" N CYS A 336 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER A 346 " --> pdb=" O CYS A 336 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 104 removed outlier: 6.025A pdb=" N LEU B 296 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ALA B 327 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE B 298 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET B 326 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY B 77 " --> pdb=" O THR B 328 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 355 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 242 removed outlier: 3.684A pdb=" N ARG B 130 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU B 290 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 134 through 137 removed outlier: 3.915A pdb=" N LYS B 234 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 141 through 142 removed outlier: 4.251A pdb=" N GLU B 141 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 164 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 381 through 382 removed outlier: 7.608A pdb=" N GLU B 381 " --> pdb=" O VAL B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 93 through 96 removed outlier: 6.441A pdb=" N CYS C 94 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ASP C 302 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N MET C 96 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL C 66 " --> pdb=" O PHE C 329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 232 through 239 Processing sheet with id=AB4, first strand: chain 'C' and resid 158 through 162 removed outlier: 3.942A pdb=" N ILE C 159 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 170 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AB6, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.426A pdb=" N VAL D 73 " --> pdb=" O MET D 326 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 236 through 243 removed outlier: 3.681A pdb=" N LYS D 236 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR D 135 " --> pdb=" O LYS D 236 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 141 through 145 removed outlier: 3.553A pdb=" N LEU D 161 " --> pdb=" O TYR D 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 332 through 334 removed outlier: 3.613A pdb=" N THR D 333 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER D 342 " --> pdb=" O THR D 333 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 93 through 95 removed outlier: 4.085A pdb=" N CYS E 94 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE E 300 " --> pdb=" O CYS E 94 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL E 66 " --> pdb=" O PHE E 329 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 230 through 239 Processing sheet with id=AC3, first strand: chain 'E' and resid 134 through 137 removed outlier: 3.571A pdb=" N THR E 136 " --> pdb=" O GLY E 160 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 100 through 103 removed outlier: 6.966A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 192 through 197 removed outlier: 7.609A pdb=" N GLU F 136 " --> pdb=" O LYS F 197 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 192 through 197 removed outlier: 7.609A pdb=" N GLU F 136 " --> pdb=" O LYS F 197 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 13 through 16 removed outlier: 5.976A pdb=" N LEU G 4 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE G 93 " --> pdb=" O LEU G 123 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 171 through 173 removed outlier: 3.745A pdb=" N VAL G 350 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU G 319 " --> pdb=" O VAL G 350 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 854 through 859 removed outlier: 4.366A pdb=" N ARG H2165 " --> pdb=" O HIS H 855 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE H 857 " --> pdb=" O ARG H2165 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE H2167 " --> pdb=" O ILE H 857 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 2062 through 2066 906 hydrogen bonds defined for protein. 2616 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: 7.28 Time building geometry restraints manager: 9.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7984 1.34 - 1.46: 2926 1.46 - 1.57: 13490 1.57 - 1.69: 0 1.69 - 1.81: 191 Bond restraints: 24591 Sorted by residual: bond pdb=" N PRO A 174 " pdb=" CD PRO A 174 " ideal model delta sigma weight residual 1.473 1.544 -0.071 1.40e-02 5.10e+03 2.61e+01 bond pdb=" N PRO G 306 " pdb=" CD PRO G 306 " ideal model delta sigma weight residual 1.473 1.544 -0.071 1.40e-02 5.10e+03 2.60e+01 bond pdb=" N PRO G 51 " pdb=" CD PRO G 51 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.24e+01 bond pdb=" C ASP A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.51e-02 4.39e+03 2.15e+01 bond pdb=" C SER H1934 " pdb=" N PRO H1935 " ideal model delta sigma weight residual 1.334 1.380 -0.046 1.11e-02 8.12e+03 1.71e+01 ... (remaining 24586 not shown) Histogram of bond angle deviations from ideal: 99.43 - 107.87: 835 107.87 - 116.30: 16088 116.30 - 124.74: 15899 124.74 - 133.18: 334 133.18 - 141.61: 15 Bond angle restraints: 33171 Sorted by residual: angle pdb=" C ILE G 294 " pdb=" N PRO G 295 " pdb=" CA PRO G 295 " ideal model delta sigma weight residual 119.47 131.15 -11.68 1.16e+00 7.43e-01 1.01e+02 angle pdb=" C PHE H1961 " pdb=" N PRO H1962 " pdb=" CA PRO H1962 " ideal model delta sigma weight residual 119.84 130.51 -10.67 1.25e+00 6.40e-01 7.28e+01 angle pdb=" C ILE H 949 " pdb=" CA ILE H 949 " pdb=" CB ILE H 949 " ideal model delta sigma weight residual 111.74 104.53 7.21 9.40e-01 1.13e+00 5.88e+01 angle pdb=" N GLU G 308 " pdb=" CA GLU G 308 " pdb=" C GLU G 308 " ideal model delta sigma weight residual 113.28 104.68 8.60 1.22e+00 6.72e-01 4.97e+01 angle pdb=" N GLU G 291 " pdb=" CA GLU G 291 " pdb=" C GLU G 291 " ideal model delta sigma weight residual 109.79 120.75 -10.96 1.56e+00 4.11e-01 4.93e+01 ... (remaining 33166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 14565 17.62 - 35.23: 449 35.23 - 52.85: 99 52.85 - 70.47: 27 70.47 - 88.08: 10 Dihedral angle restraints: 15150 sinusoidal: 6170 harmonic: 8980 Sorted by residual: dihedral pdb=" CA ASN G 354 " pdb=" C ASN G 354 " pdb=" N PRO G 355 " pdb=" CA PRO G 355 " ideal model delta harmonic sigma weight residual 180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA LYS F 164 " pdb=" C LYS F 164 " pdb=" N THR F 165 " pdb=" CA THR F 165 " ideal model delta harmonic sigma weight residual -180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA PRO H1935 " pdb=" C PRO H1935 " pdb=" N ILE H1936 " pdb=" CA ILE H1936 " ideal model delta harmonic sigma weight residual 180.00 152.56 27.44 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 15147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3331 0.071 - 0.142: 492 0.142 - 0.213: 49 0.213 - 0.284: 11 0.284 - 0.355: 2 Chirality restraints: 3885 Sorted by residual: chirality pdb=" CB ILE C 193 " pdb=" CA ILE C 193 " pdb=" CG1 ILE C 193 " pdb=" CG2 ILE C 193 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA GLU G 291 " pdb=" N GLU G 291 " pdb=" C GLU G 291 " pdb=" CB GLU G 291 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA ILE G 57 " pdb=" N ILE G 57 " pdb=" C ILE G 57 " pdb=" CB ILE G 57 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 3882 not shown) Planarity restraints: 4263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU H 948 " -0.022 2.00e-02 2.50e+03 4.40e-02 1.94e+01 pdb=" C LEU H 948 " 0.076 2.00e-02 2.50e+03 pdb=" O LEU H 948 " -0.029 2.00e-02 2.50e+03 pdb=" N ILE H 949 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS H 936 " 0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO H 937 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO H 937 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO H 937 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H1930 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.78e+00 pdb=" N PRO H1931 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO H1931 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO H1931 " -0.039 5.00e-02 4.00e+02 ... (remaining 4260 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 53 1.82 - 2.59: 370 2.59 - 3.36: 28681 3.36 - 4.13: 52538 4.13 - 4.90: 92292 Nonbonded interactions: 173934 Sorted by model distance: nonbonded pdb=" NH2 ARG D 284 " pdb=" CB ILE D 291 " model vdw 1.054 3.550 nonbonded pdb=" C ALA G 42 " pdb=" CG ASP G 46 " model vdw 1.101 3.500 nonbonded pdb=" O ALA G 42 " pdb=" OD2 ASP G 46 " model vdw 1.153 3.040 nonbonded pdb=" CD1 ILE A 279 " pdb=" NH1 ARG H 945 " model vdw 1.158 3.540 nonbonded pdb=" OE2 GLU F 144 " pdb=" O LYS F 160 " model vdw 1.177 3.040 ... (remaining 173929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 136 or resid 157 through 178 or resid 189 throu \ gh 194 or resid 224 through 443)) selection = (chain 'C' and (resid 13 through 194 or resid 224 through 250 or resid 269 throu \ gh 443)) selection = (chain 'E' and (resid 13 through 136 or resid 157 through 178 or resid 189 throu \ gh 194 or resid 224 through 250 or resid 269 through 443)) } ncs_group { reference = (chain 'B' and (resid 18 through 94 or resid 98 through 146 or resid 159 through \ 172 or resid 175 or resid 191 through 197 or resid 232 through 261 or resid 265 \ through 447)) selection = (chain 'D' and (resid 18 through 94 or resid 98 through 172 or resid 175 or resi \ d 191 through 197 or resid 232 through 447)) selection = (chain 'F' and (resid 18 through 172 or resid 190 through 261 or resid 265 throu \ gh 447)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 0.030 Extract box with map and model: 7.880 Check model and map are aligned: 0.380 Set scattering table: 0.210 Process input model: 58.250 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 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 0.073 24591 Z= 0.227 Angle : 0.881 16.613 33171 Z= 0.505 Chirality : 0.052 0.355 3885 Planarity : 0.006 0.087 4263 Dihedral : 10.126 88.083 9332 Min Nonbonded Distance : 1.054 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 1.10 % Allowed : 7.26 % Favored : 91.63 % Rotamer: Outliers : 2.70 % Allowed : 1.98 % Favored : 95.32 % 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: -4.30 (0.12), residues: 2988 helix: -2.90 (0.10), residues: 1179 sheet: -1.18 (0.23), residues: 448 loop : -3.38 (0.13), residues: 1361 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1004 time to evaluate : 2.787 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 23 residues processed: 1062 average time/residue: 0.4242 time to fit residues: 659.3427 Evaluate side-chains 507 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 484 time to evaluate : 2.708 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 5 residues processed: 23 average time/residue: 0.2695 time to fit residues: 14.1625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 129 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 124 optimal weight: 0.0970 chunk 241 optimal weight: 0.9980 chunk 93 optimal weight: 0.3980 chunk 146 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 chunk 279 optimal weight: 0.0980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 393 HIS A 429 HIS B 41 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 236 GLN C 241 HIS ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 GLN C 393 HIS C 414 ASN C 429 HIS D 240 HIS D 245 HIS ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS E 42 GLN E 284 ASN E 332 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN F 447 GLN G 21 ASN ** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 HIS H 865 GLN H 967 HIS ** H1964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H2060 HIS H2153 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24591 Z= 0.208 Angle : 0.713 10.016 33171 Z= 0.361 Chirality : 0.046 0.253 3885 Planarity : 0.005 0.107 4263 Dihedral : 4.945 26.846 3354 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.36 % Favored : 93.47 % Rotamer: Outliers : 3.73 % Allowed : 14.04 % Favored : 82.24 % 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: -2.70 (0.14), residues: 2988 helix: -1.07 (0.14), residues: 1199 sheet: -0.74 (0.22), residues: 468 loop : -2.90 (0.15), residues: 1321 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 525 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 53 residues processed: 587 average time/residue: 0.3654 time to fit residues: 333.0474 Evaluate side-chains 463 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 410 time to evaluate : 2.734 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.2327 time to fit residues: 26.8042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 232 optimal weight: 0.0770 chunk 190 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 280 optimal weight: 0.3980 chunk 302 optimal weight: 6.9990 chunk 249 optimal weight: 0.0170 chunk 277 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 224 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 HIS D 240 HIS E 18 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN ** G 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 323 ASN H 865 GLN ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H2082 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24591 Z= 0.195 Angle : 0.666 9.584 33171 Z= 0.335 Chirality : 0.045 0.425 3885 Planarity : 0.005 0.067 4263 Dihedral : 4.705 30.163 3354 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.93 % Favored : 92.94 % Rotamer: Outliers : 2.85 % Allowed : 16.36 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.87 (0.15), residues: 2988 helix: -0.07 (0.15), residues: 1208 sheet: -0.48 (0.23), residues: 465 loop : -2.72 (0.15), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 457 time to evaluate : 2.876 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 outliers start: 75 outliers final: 34 residues processed: 503 average time/residue: 0.3314 time to fit residues: 263.4423 Evaluate side-chains 422 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 388 time to evaluate : 2.747 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2151 time to fit residues: 17.5225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 281 optimal weight: 0.0870 chunk 297 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 229 HIS A 247 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 HIS D 25 HIS ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 HIS ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN G 61 GLN G 139 ASN H 902 ASN ** H1964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H2031 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.7504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 24591 Z= 0.338 Angle : 0.803 12.402 33171 Z= 0.407 Chirality : 0.049 0.540 3885 Planarity : 0.005 0.069 4263 Dihedral : 5.311 31.872 3354 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.40 % Favored : 92.40 % Rotamer: Outliers : 4.37 % Allowed : 17.08 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.75 (0.15), residues: 2988 helix: 0.10 (0.15), residues: 1206 sheet: -0.55 (0.23), residues: 472 loop : -2.68 (0.15), residues: 1310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 424 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 53 residues processed: 496 average time/residue: 0.3392 time to fit residues: 267.1580 Evaluate side-chains 390 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 337 time to evaluate : 2.648 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.2146 time to fit residues: 24.9199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 221 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 254 optimal weight: 0.0870 chunk 205 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 267 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN B 341 GLN ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN G 204 GLN G 385 ASN H 936 HIS ** H1964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1968 GLN ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.7896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24591 Z= 0.197 Angle : 0.680 10.317 33171 Z= 0.337 Chirality : 0.046 0.466 3885 Planarity : 0.004 0.058 4263 Dihedral : 4.881 31.758 3354 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.76 % Favored : 93.11 % Rotamer: Outliers : 2.51 % Allowed : 20.08 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.44 (0.15), residues: 2988 helix: 0.41 (0.15), residues: 1212 sheet: -0.41 (0.23), residues: 453 loop : -2.53 (0.15), residues: 1323 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 389 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 30 residues processed: 428 average time/residue: 0.3401 time to fit residues: 233.5938 Evaluate side-chains 370 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 340 time to evaluate : 3.300 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3180 time to fit residues: 21.4336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 0.0670 chunk 268 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 24 optimal weight: 0.0570 chunk 98 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 323 ASN ** H 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.8342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24591 Z= 0.220 Angle : 0.693 13.568 33171 Z= 0.342 Chirality : 0.045 0.324 3885 Planarity : 0.004 0.075 4263 Dihedral : 4.846 31.558 3354 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.86 % Favored : 93.07 % Rotamer: Outliers : 2.17 % Allowed : 22.10 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.30 (0.15), residues: 2988 helix: 0.55 (0.15), residues: 1213 sheet: -0.48 (0.23), residues: 470 loop : -2.45 (0.16), residues: 1305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 388 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 30 residues processed: 426 average time/residue: 0.3550 time to fit residues: 245.9197 Evaluate side-chains 371 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 341 time to evaluate : 2.936 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2458 time to fit residues: 17.3459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 217 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 chunk 185 optimal weight: 0.0170 chunk 180 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 HIS ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1968 GLN ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.8903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24591 Z= 0.249 Angle : 0.714 12.332 33171 Z= 0.356 Chirality : 0.046 0.266 3885 Planarity : 0.004 0.062 4263 Dihedral : 4.938 31.951 3354 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.53 % Favored : 92.40 % Rotamer: Outliers : 2.24 % Allowed : 23.05 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.22 (0.15), residues: 2988 helix: 0.62 (0.15), residues: 1206 sheet: -0.42 (0.24), residues: 474 loop : -2.40 (0.16), residues: 1308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 379 time to evaluate : 2.728 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 outliers start: 59 outliers final: 28 residues processed: 409 average time/residue: 0.3348 time to fit residues: 219.7849 Evaluate side-chains 374 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 346 time to evaluate : 2.829 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2269 time to fit residues: 15.5432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 233 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS C 236 GLN ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 GLN ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 GLN G 385 ASN H 902 ASN ** H1964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.9622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24591 Z= 0.306 Angle : 0.788 15.804 33171 Z= 0.392 Chirality : 0.048 0.278 3885 Planarity : 0.005 0.073 4263 Dihedral : 5.266 32.688 3354 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.47 % Favored : 91.47 % Rotamer: Outliers : 1.94 % Allowed : 23.32 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.15), residues: 2988 helix: 0.55 (0.15), residues: 1212 sheet: -0.59 (0.23), residues: 472 loop : -2.44 (0.16), residues: 1304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 366 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 19 residues processed: 398 average time/residue: 0.3546 time to fit residues: 221.9658 Evaluate side-chains 344 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 325 time to evaluate : 2.734 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2342 time to fit residues: 11.9772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 4.9990 chunk 284 optimal weight: 0.9990 chunk 259 optimal weight: 0.7980 chunk 276 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 120 optimal weight: 0.5980 chunk 217 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 249 optimal weight: 0.9980 chunk 261 optimal weight: 0.5980 chunk 275 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN G 19 HIS G 118 GLN ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 GLN G 387 HIS ** H1964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.9775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24591 Z= 0.223 Angle : 0.752 14.735 33171 Z= 0.369 Chirality : 0.047 0.383 3885 Planarity : 0.004 0.057 4263 Dihedral : 5.042 33.761 3354 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.66 % Favored : 92.30 % Rotamer: Outliers : 0.99 % Allowed : 25.33 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 2988 helix: 0.63 (0.15), residues: 1215 sheet: -0.36 (0.24), residues: 442 loop : -2.39 (0.16), residues: 1331 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 353 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 371 average time/residue: 0.3587 time to fit residues: 211.1703 Evaluate side-chains 338 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 326 time to evaluate : 2.839 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2142 time to fit residues: 8.8359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 0.2980 chunk 292 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 203 optimal weight: 2.9990 chunk 306 optimal weight: 4.9990 chunk 282 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 149 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 HIS ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.9913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24591 Z= 0.209 Angle : 0.738 16.359 33171 Z= 0.359 Chirality : 0.046 0.326 3885 Planarity : 0.004 0.058 4263 Dihedral : 4.898 34.201 3354 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.53 % Favored : 92.44 % Rotamer: Outliers : 0.34 % Allowed : 26.21 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.06 (0.16), residues: 2988 helix: 0.74 (0.16), residues: 1211 sheet: -0.41 (0.24), residues: 467 loop : -2.27 (0.16), residues: 1310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 362 time to evaluate : 2.865 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: 9 outliers final: 4 residues processed: 365 average time/residue: 0.3533 time to fit residues: 204.7599 Evaluate side-chains 338 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 334 time to evaluate : 2.655 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2036 time to fit residues: 5.3683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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: 55.8613 > 50: distance: 60 - 80: 9.674 distance: 75 - 80: 7.752 distance: 80 - 81: 9.570 distance: 81 - 82: 15.441 distance: 81 - 84: 13.739 distance: 82 - 83: 16.693 distance: 82 - 91: 4.742 distance: 84 - 85: 8.411 distance: 86 - 87: 8.913 distance: 87 - 88: 7.868 distance: 88 - 89: 9.384 distance: 88 - 90: 8.822 distance: 91 - 92: 5.080 distance: 92 - 93: 21.562 distance: 92 - 95: 3.453 distance: 93 - 94: 33.271 distance: 93 - 97: 9.044 distance: 95 - 96: 29.059 distance: 97 - 98: 11.101 distance: 98 - 99: 10.669 distance: 98 - 101: 24.701 distance: 99 - 100: 18.095 distance: 99 - 105: 11.637 distance: 101 - 102: 20.489 distance: 102 - 103: 21.663 distance: 102 - 104: 18.346 distance: 105 - 106: 15.496 distance: 106 - 107: 9.847 distance: 106 - 109: 5.420 distance: 107 - 108: 18.799 distance: 107 - 112: 9.010 distance: 109 - 110: 23.177 distance: 109 - 111: 20.995 distance: 112 - 113: 14.009 distance: 112 - 118: 5.573 distance: 113 - 114: 8.304 distance: 113 - 116: 8.432 distance: 114 - 115: 17.897 distance: 114 - 119: 6.974 distance: 116 - 117: 8.440 distance: 117 - 118: 13.179 distance: 119 - 120: 5.922 distance: 120 - 121: 6.833 distance: 120 - 123: 6.885 distance: 121 - 122: 22.498 distance: 121 - 126: 19.958 distance: 123 - 124: 18.865 distance: 123 - 125: 24.815 distance: 126 - 127: 11.510 distance: 127 - 128: 11.695 distance: 127 - 130: 13.205 distance: 128 - 129: 18.269 distance: 128 - 134: 11.147 distance: 130 - 131: 7.055 distance: 131 - 132: 10.338 distance: 131 - 133: 16.953 distance: 134 - 135: 14.275 distance: 135 - 136: 8.158 distance: 135 - 138: 10.956 distance: 136 - 137: 33.545 distance: 136 - 146: 6.893 distance: 138 - 139: 7.260 distance: 139 - 140: 7.268 distance: 139 - 141: 6.587 distance: 140 - 142: 11.227 distance: 141 - 143: 5.462 distance: 142 - 144: 6.102 distance: 143 - 144: 13.723 distance: 144 - 145: 11.159 distance: 146 - 147: 18.567 distance: 147 - 148: 10.877 distance: 147 - 150: 15.973 distance: 148 - 149: 10.337 distance: 148 - 154: 9.284 distance: 150 - 151: 19.735 distance: 151 - 152: 16.243 distance: 151 - 153: 12.015 distance: 154 - 155: 8.188 distance: 155 - 156: 7.006 distance: 155 - 158: 5.249 distance: 156 - 157: 8.260 distance: 158 - 159: 19.958 distance: 158 - 160: 16.954