Starting phenix.real_space_refine on Tue Mar 19 12:43:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6igm_9668/03_2024/6igm_9668.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6igm_9668/03_2024/6igm_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_9668/03_2024/6igm_9668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6igm_9668/03_2024/6igm_9668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6igm_9668/03_2024/6igm_9668.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6igm_9668/03_2024/6igm_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.91, per 1000 atoms: 0.53 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: 8.59 Conformation dependent library (CDL) restraints added in 6.1 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: 2.49 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: 8.01 Time building geometry restraints manager: 9.45 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: 1.500 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: 8.000 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 67.960 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.120 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.160 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H1998 HIS 0.006 0.001 HIS E 316 PHE 0.025 0.002 PHE H 963 TYR 0.024 0.001 TYR B 387 ARG 0.008 0.000 ARG G 124 *********************** 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 : 2.733 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 REVERT: A 96 MET cc_start: 0.8765 (ttp) cc_final: 0.8322 (ttm) REVERT: A 100 GLU cc_start: 0.6906 (tt0) cc_final: 0.6289 (tp30) REVERT: A 170 LEU cc_start: 0.7239 (tp) cc_final: 0.5926 (tp) REVERT: A 333 ARG cc_start: 0.5970 (ptp90) cc_final: 0.5341 (tpm170) REVERT: B 178 MET cc_start: 0.6736 (mmm) cc_final: 0.6230 (tpp) REVERT: B 299 ASP cc_start: 0.8027 (m-30) cc_final: 0.7615 (t0) REVERT: B 420 GLU cc_start: 0.6113 (tt0) cc_final: 0.5870 (pm20) REVERT: C 91 VAL cc_start: 0.9087 (t) cc_final: 0.8827 (t) REVERT: C 129 GLU cc_start: 0.6136 (pm20) cc_final: 0.4511 (tm-30) REVERT: C 173 ASP cc_start: 0.7428 (m-30) cc_final: 0.7181 (m-30) REVERT: C 299 LEU cc_start: 0.8706 (tp) cc_final: 0.8376 (tp) REVERT: C 314 TYR cc_start: 0.6924 (t80) cc_final: 0.6058 (t80) REVERT: C 322 SER cc_start: 0.8464 (p) cc_final: 0.8077 (m) REVERT: C 356 ASP cc_start: 0.7855 (t0) cc_final: 0.7530 (t70) REVERT: D 172 TYR cc_start: 0.7167 (m-80) cc_final: 0.6922 (t80) REVERT: D 269 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7425 (pttp) REVERT: D 435 ASP cc_start: 0.6110 (m-30) cc_final: 0.5075 (m-30) REVERT: E 49 CYS cc_start: 0.7856 (p) cc_final: 0.7429 (t) REVERT: E 89 SER cc_start: 0.8277 (m) cc_final: 0.8011 (p) REVERT: E 278 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7459 (tt0) REVERT: F 121 GLN cc_start: 0.7725 (mt0) cc_final: 0.7215 (tp40) REVERT: F 132 LYS cc_start: 0.7377 (ttpp) cc_final: 0.6980 (tmmt) REVERT: F 144 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.3463 (mp0) REVERT: F 326 MET cc_start: 0.8320 (mmt) cc_final: 0.8005 (mmm) REVERT: G 43 ASN cc_start: 0.5425 (t0) cc_final: 0.4374 (p0) REVERT: G 72 ARG cc_start: 0.7537 (ptp-170) cc_final: 0.6581 (ptm-80) REVERT: G 96 THR cc_start: 0.5432 (p) cc_final: 0.5139 (p) REVERT: G 111 GLU cc_start: 0.8754 (tt0) cc_final: 0.8458 (tp30) REVERT: G 205 VAL cc_start: 0.6930 (t) cc_final: 0.6378 (p) REVERT: G 269 ARG cc_start: 0.7511 (tpp-160) cc_final: 0.7266 (tpp80) REVERT: G 291 GLU cc_start: 0.0751 (OUTLIER) cc_final: -0.0127 (tp30) REVERT: H 902 ASN cc_start: 0.5869 (m-40) cc_final: 0.5274 (m-40) REVERT: H 913 THR cc_start: 0.6991 (m) cc_final: 0.6618 (m) REVERT: H 934 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7138 (m-30) REVERT: H 940 ARG cc_start: 0.4255 (OUTLIER) cc_final: 0.2006 (ptt-90) REVERT: H 951 LEU cc_start: 0.5176 (OUTLIER) cc_final: 0.4798 (mt) REVERT: H 952 GLU cc_start: 0.4584 (OUTLIER) cc_final: 0.3834 (mm-30) REVERT: H 954 ARG cc_start: 0.5734 (mtt180) cc_final: 0.5500 (mtp85) REVERT: H 2024 ILE cc_start: 0.8609 (mm) cc_final: 0.8402 (mp) REVERT: H 2038 ILE cc_start: 0.6794 (mt) cc_final: 0.6562 (mt) REVERT: H 2102 MET cc_start: 0.5245 (mmm) cc_final: 0.4949 (tpp) outliers start: 71 outliers final: 23 residues processed: 1062 average time/residue: 0.4126 time to fit residues: 636.2986 Evaluate side-chains 526 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 496 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 236 TYR Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 934 ASP Chi-restraints excluded: chain H residue 935 VAL Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 940 ARG Chi-restraints excluded: chain H residue 943 MET Chi-restraints excluded: chain H residue 951 LEU Chi-restraints excluded: chain H residue 952 GLU Chi-restraints excluded: chain H residue 2027 ASN Chi-restraints excluded: chain H residue 2028 MET Chi-restraints excluded: chain H residue 2037 LEU 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: 0.3980 chunk 129 optimal weight: 6.9990 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: 6.9990 chunk 146 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 chunk 279 optimal weight: 0.0030 overall best weight: 0.4388 ------------------------------------------------------------------------------- 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 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** H2022 HIS H2060 HIS H2153 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.4512 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= 0.206 Angle : 0.707 10.060 33171 Z= 0.358 Chirality : 0.045 0.197 3885 Planarity : 0.005 0.107 4263 Dihedral : 6.747 104.104 3427 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.69 % Favored : 93.14 % Rotamer: Outliers : 4.11 % Allowed : 13.50 % Favored : 82.39 % 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: -1.03 (0.14), residues: 1191 sheet: -0.78 (0.22), residues: 468 loop : -2.90 (0.15), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H2015 HIS 0.009 0.001 HIS D 240 PHE 0.027 0.002 PHE H 872 TYR 0.026 0.002 TYR G 77 ARG 0.008 0.001 ARG G 269 *********************** 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 639 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 531 time to evaluate : 2.973 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: A 46 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6308 (mmm-85) REVERT: A 96 MET cc_start: 0.8627 (ttp) cc_final: 0.8194 (ttm) REVERT: A 100 GLU cc_start: 0.7016 (tt0) cc_final: 0.6429 (tp30) REVERT: A 124 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7669 (pp) REVERT: A 333 ARG cc_start: 0.6227 (ptp90) cc_final: 0.5583 (tpm170) REVERT: A 406 SER cc_start: 0.8822 (p) cc_final: 0.8483 (t) REVERT: B 107 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7647 (mp0) REVERT: B 196 ASP cc_start: 0.7923 (p0) cc_final: 0.7532 (p0) REVERT: B 299 ASP cc_start: 0.8127 (m-30) cc_final: 0.7817 (t0) REVERT: B 420 GLU cc_start: 0.6470 (tt0) cc_final: 0.6175 (pm20) REVERT: C 173 ASP cc_start: 0.7470 (m-30) cc_final: 0.7112 (m-30) REVERT: C 271 ILE cc_start: 0.8748 (mt) cc_final: 0.8538 (mt) REVERT: C 322 SER cc_start: 0.8581 (p) cc_final: 0.8259 (m) REVERT: C 432 GLU cc_start: 0.8483 (tt0) cc_final: 0.8238 (tp30) REVERT: D 46 MET cc_start: 0.7487 (mmm) cc_final: 0.7211 (tpt) REVERT: D 169 GLU cc_start: 0.5524 (mm-30) cc_final: 0.4913 (mm-30) REVERT: D 172 TYR cc_start: 0.7380 (m-80) cc_final: 0.6920 (t80) REVERT: D 237 GLU cc_start: 0.6511 (mm-30) cc_final: 0.5155 (tp30) REVERT: D 279 LYS cc_start: 0.6574 (ptmt) cc_final: 0.6134 (ptmt) REVERT: D 441 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7466 (mp10) REVERT: E 49 CYS cc_start: 0.8121 (p) cc_final: 0.7593 (t) REVERT: E 278 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7425 (tt0) REVERT: F 168 MET cc_start: 0.5363 (mpp) cc_final: 0.5106 (ttt) REVERT: F 285 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7962 (mm-30) REVERT: F 334 ARG cc_start: 0.7132 (ttp80) cc_final: 0.6887 (mmp80) REVERT: F 411 LEU cc_start: 0.7695 (pt) cc_final: 0.7489 (pp) REVERT: G 1 MET cc_start: 0.2309 (ppp) cc_final: 0.2056 (ppp) REVERT: G 43 ASN cc_start: 0.5906 (t0) cc_final: 0.4111 (p0) REVERT: G 79 PHE cc_start: 0.4887 (m-10) cc_final: 0.4681 (m-10) REVERT: G 204 GLN cc_start: 0.8007 (mt0) cc_final: 0.7668 (tm-30) REVERT: G 270 LEU cc_start: 0.5217 (OUTLIER) cc_final: 0.4849 (tt) REVERT: H 1903 ARG cc_start: 0.7412 (mmm-85) cc_final: 0.7182 (mmm-85) REVERT: H 2027 ASN cc_start: 0.7196 (OUTLIER) cc_final: 0.6911 (p0) outliers start: 108 outliers final: 54 residues processed: 603 average time/residue: 0.3592 time to fit residues: 332.7309 Evaluate side-chains 472 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 413 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 934 ASP Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 2025 VAL Chi-restraints excluded: chain H residue 2027 ASN Chi-restraints excluded: chain H residue 2028 MET Chi-restraints excluded: chain H residue 2152 CYS Chi-restraints excluded: chain H residue 2189 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 232 optimal weight: 0.0370 chunk 190 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 280 optimal weight: 0.6980 chunk 302 optimal weight: 6.9990 chunk 249 optimal weight: 0.8980 chunk 277 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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** C 414 ASN D 25 HIS D 240 HIS ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 HIS G 118 GLN ** G 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 323 ASN H 865 GLN ** H 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H2082 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 24591 Z= 0.212 Angle : 0.668 9.001 33171 Z= 0.337 Chirality : 0.045 0.631 3885 Planarity : 0.005 0.070 4263 Dihedral : 5.226 54.504 3371 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.96 % Favored : 92.90 % Rotamer: Outliers : 4.45 % Allowed : 15.94 % Favored : 79.61 % 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: -1.92 (0.15), residues: 2988 helix: -0.14 (0.15), residues: 1210 sheet: -0.54 (0.23), residues: 471 loop : -2.71 (0.15), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H2015 HIS 0.008 0.001 HIS A 316 PHE 0.020 0.001 PHE H1978 TYR 0.038 0.002 TYR G 77 ARG 0.010 0.001 ARG B 64 *********************** 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 561 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 444 time to evaluate : 2.862 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: A 96 MET cc_start: 0.8594 (ttp) cc_final: 0.8133 (ttm) REVERT: A 100 GLU cc_start: 0.7186 (tt0) cc_final: 0.6608 (tp30) REVERT: A 124 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7854 (pp) REVERT: A 218 GLU cc_start: 0.6514 (mm-30) cc_final: 0.6241 (mm-30) REVERT: A 235 ILE cc_start: 0.6992 (mt) cc_final: 0.6554 (pt) REVERT: A 333 ARG cc_start: 0.6908 (ptp90) cc_final: 0.6043 (tpm170) REVERT: B 106 SER cc_start: 0.9203 (p) cc_final: 0.8914 (m) REVERT: B 107 GLU cc_start: 0.8064 (mm-30) cc_final: 0.6977 (mp0) REVERT: B 196 ASP cc_start: 0.7858 (p0) cc_final: 0.7411 (p0) REVERT: B 290 GLU cc_start: 0.8467 (pm20) cc_final: 0.8261 (pm20) REVERT: B 420 GLU cc_start: 0.6601 (tt0) cc_final: 0.6257 (pm20) REVERT: B 428 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7679 (ttp80) REVERT: B 443 MET cc_start: 0.7929 (mmp) cc_final: 0.6772 (mtt) REVERT: C 96 MET cc_start: 0.7467 (ttm) cc_final: 0.7005 (ttm) REVERT: C 322 SER cc_start: 0.8597 (p) cc_final: 0.8252 (m) REVERT: C 432 GLU cc_start: 0.8411 (tt0) cc_final: 0.8168 (tp30) REVERT: D 46 MET cc_start: 0.7717 (mmm) cc_final: 0.7466 (tpt) REVERT: D 172 TYR cc_start: 0.7248 (m-80) cc_final: 0.6919 (t80) REVERT: D 232 LEU cc_start: 0.4999 (OUTLIER) cc_final: 0.4744 (tp) REVERT: D 237 GLU cc_start: 0.6654 (mm-30) cc_final: 0.5454 (tp30) REVERT: D 405 LEU cc_start: 0.8588 (tp) cc_final: 0.8249 (tp) REVERT: E 49 CYS cc_start: 0.8205 (p) cc_final: 0.7668 (t) REVERT: E 278 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7527 (tt0) REVERT: E 388 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6837 (mm-30) REVERT: F 145 ILE cc_start: 0.6245 (OUTLIER) cc_final: 0.6044 (pp) REVERT: F 285 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8072 (mm-30) REVERT: F 300 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6384 (mt-10) REVERT: F 325 ILE cc_start: 0.8887 (mt) cc_final: 0.8679 (mt) REVERT: F 334 ARG cc_start: 0.7556 (ttp80) cc_final: 0.7214 (mmp80) REVERT: F 403 ILE cc_start: 0.9179 (mt) cc_final: 0.8907 (mt) REVERT: F 411 LEU cc_start: 0.7726 (pt) cc_final: 0.7480 (pp) REVERT: G 1 MET cc_start: 0.2508 (ppp) cc_final: 0.1803 (ppp) REVERT: G 43 ASN cc_start: 0.5827 (t0) cc_final: 0.4157 (p0) REVERT: G 79 PHE cc_start: 0.5065 (m-10) cc_final: 0.4822 (m-10) REVERT: G 204 GLN cc_start: 0.8065 (mt0) cc_final: 0.7639 (tm-30) REVERT: G 220 MET cc_start: 0.7512 (mmt) cc_final: 0.7159 (mmt) REVERT: G 221 ASP cc_start: 0.8695 (t70) cc_final: 0.8402 (t0) REVERT: H 949 ILE cc_start: 0.4675 (OUTLIER) cc_final: 0.4233 (mm) REVERT: H 1930 GLN cc_start: 0.8060 (pp30) cc_final: 0.7822 (pp30) outliers start: 117 outliers final: 75 residues processed: 525 average time/residue: 0.3509 time to fit residues: 290.8735 Evaluate side-chains 477 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 396 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 229 HIS Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 934 ASP Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 938 LEU Chi-restraints excluded: chain H residue 949 ILE Chi-restraints excluded: chain H residue 1922 VAL Chi-restraints excluded: chain H residue 1999 LEU Chi-restraints excluded: chain H residue 2152 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 0.9980 chunk 210 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 281 optimal weight: 3.9990 chunk 297 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 chunk 266 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 HIS ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 HIS E 18 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 GLN ** G 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24591 Z= 0.273 Angle : 0.720 8.836 33171 Z= 0.364 Chirality : 0.047 0.504 3885 Planarity : 0.005 0.069 4263 Dihedral : 5.414 46.769 3366 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.13 % Favored : 92.74 % Rotamer: Outliers : 5.97 % Allowed : 16.32 % Favored : 77.71 % 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: -1.54 (0.15), residues: 2988 helix: 0.29 (0.15), residues: 1205 sheet: -0.36 (0.24), residues: 450 loop : -2.57 (0.15), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H2015 HIS 0.009 0.002 HIS B 240 PHE 0.031 0.002 PHE E 177 TYR 0.041 0.002 TYR G 77 ARG 0.011 0.001 ARG H2002 *********************** 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 586 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 429 time to evaluate : 2.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8582 (ttp) cc_final: 0.8372 (ttp) REVERT: A 100 GLU cc_start: 0.7374 (tt0) cc_final: 0.6959 (tp30) REVERT: A 124 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8082 (pp) REVERT: A 131 TYR cc_start: 0.8344 (m-80) cc_final: 0.8074 (m-10) REVERT: A 218 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6237 (mm-30) REVERT: A 219 GLU cc_start: 0.4709 (pm20) cc_final: 0.4486 (mm-30) REVERT: A 235 ILE cc_start: 0.7647 (mt) cc_final: 0.7172 (pt) REVERT: A 354 LEU cc_start: 0.8399 (tp) cc_final: 0.8167 (tp) REVERT: B 106 SER cc_start: 0.9116 (p) cc_final: 0.8398 (m) REVERT: B 107 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 191 ASP cc_start: 0.3815 (OUTLIER) cc_final: 0.3188 (p0) REVERT: B 239 VAL cc_start: 0.9068 (t) cc_final: 0.8862 (p) REVERT: B 245 HIS cc_start: 0.7824 (m90) cc_final: 0.7621 (m90) REVERT: B 320 MET cc_start: 0.7848 (mmp) cc_final: 0.7444 (mmt) REVERT: B 443 MET cc_start: 0.8087 (mmp) cc_final: 0.7416 (ttt) REVERT: C 85 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8165 (mt0) REVERT: C 242 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7748 (m-30) REVERT: C 431 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8137 (pp20) REVERT: C 432 GLU cc_start: 0.8516 (tt0) cc_final: 0.7870 (tp30) REVERT: D 119 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8654 (mm) REVERT: D 237 GLU cc_start: 0.6916 (mm-30) cc_final: 0.5853 (tp30) REVERT: D 269 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7067 (tptt) REVERT: D 303 MET cc_start: 0.7961 (ppp) cc_final: 0.7701 (ppp) REVERT: D 325 ILE cc_start: 0.8634 (mt) cc_final: 0.8325 (mt) REVERT: D 405 LEU cc_start: 0.8736 (tp) cc_final: 0.8447 (tp) REVERT: E 49 CYS cc_start: 0.8162 (p) cc_final: 0.7605 (t) REVERT: E 192 TYR cc_start: 0.5676 (OUTLIER) cc_final: 0.5350 (p90) REVERT: E 278 GLU cc_start: 0.8565 (mm-30) cc_final: 0.7641 (tt0) REVERT: E 284 ASN cc_start: 0.8946 (m-40) cc_final: 0.8620 (m-40) REVERT: E 308 ASP cc_start: 0.8033 (m-30) cc_final: 0.7638 (m-30) REVERT: F 107 GLU cc_start: 0.7258 (tt0) cc_final: 0.6917 (tp30) REVERT: F 334 ARG cc_start: 0.7854 (ttp80) cc_final: 0.7212 (mmp80) REVERT: F 335 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6813 (mt) REVERT: G 1 MET cc_start: 0.2879 (ppp) cc_final: 0.2444 (ppp) REVERT: G 43 ASN cc_start: 0.5429 (t0) cc_final: 0.3430 (p0) REVERT: G 79 PHE cc_start: 0.5615 (m-10) cc_final: 0.5349 (m-10) REVERT: G 220 MET cc_start: 0.7631 (mmt) cc_final: 0.7287 (mmt) REVERT: G 221 ASP cc_start: 0.8820 (t70) cc_final: 0.8510 (t0) REVERT: H 949 ILE cc_start: 0.5247 (OUTLIER) cc_final: 0.4799 (mm) REVERT: H 2054 GLN cc_start: 0.7975 (tm-30) cc_final: 0.6697 (mt0) REVERT: H 2068 MET cc_start: 0.4143 (mtt) cc_final: 0.3934 (mtp) outliers start: 157 outliers final: 98 residues processed: 535 average time/residue: 0.3189 time to fit residues: 274.1474 Evaluate side-chains 466 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 360 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 192 TYR Chi-restraints excluded: chain E residue 229 HIS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 286 ASP Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 873 MET Chi-restraints excluded: chain H residue 934 ASP Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 938 LEU Chi-restraints excluded: chain H residue 948 LEU Chi-restraints excluded: chain H residue 949 ILE Chi-restraints excluded: chain H residue 1907 LEU Chi-restraints excluded: chain H residue 1917 VAL Chi-restraints excluded: chain H residue 1922 VAL Chi-restraints excluded: chain H residue 1999 LEU Chi-restraints excluded: chain H residue 2026 CYS Chi-restraints excluded: chain H residue 2038 ILE Chi-restraints excluded: chain H residue 2115 ILE Chi-restraints excluded: chain H residue 2152 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 221 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 254 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 267 optimal weight: 0.0670 chunk 75 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 341 GLN B 447 GLN ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN G 139 ASN ** G 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 936 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.7562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24591 Z= 0.204 Angle : 0.666 16.195 33171 Z= 0.331 Chirality : 0.045 0.387 3885 Planarity : 0.004 0.071 4263 Dihedral : 5.213 48.274 3366 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.89 % Favored : 93.01 % Rotamer: Outliers : 4.60 % Allowed : 19.82 % Favored : 75.58 % 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: -1.34 (0.15), residues: 2988 helix: 0.45 (0.15), residues: 1213 sheet: -0.32 (0.24), residues: 461 loop : -2.46 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 283 HIS 0.007 0.001 HIS A 316 PHE 0.033 0.002 PHE H1978 TYR 0.037 0.002 TYR G 77 ARG 0.018 0.001 ARG G 137 *********************** 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 519 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 398 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ILE cc_start: 0.9625 (mt) cc_final: 0.9363 (mp) REVERT: A 100 GLU cc_start: 0.7478 (tt0) cc_final: 0.7241 (tp30) REVERT: A 124 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8102 (pp) REVERT: A 192 TYR cc_start: 0.6375 (m-10) cc_final: 0.5882 (m-10) REVERT: A 218 GLU cc_start: 0.6279 (mm-30) cc_final: 0.5991 (mm-30) REVERT: A 219 GLU cc_start: 0.5082 (pm20) cc_final: 0.3210 (pm20) REVERT: A 235 ILE cc_start: 0.7405 (mt) cc_final: 0.7006 (pt) REVERT: B 106 SER cc_start: 0.9007 (p) cc_final: 0.8763 (m) REVERT: B 107 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7435 (mp0) REVERT: B 239 VAL cc_start: 0.9102 (t) cc_final: 0.8848 (p) REVERT: B 240 HIS cc_start: 0.7448 (OUTLIER) cc_final: 0.5693 (t-90) REVERT: B 290 GLU cc_start: 0.8321 (pm20) cc_final: 0.8043 (pm20) REVERT: B 320 MET cc_start: 0.7647 (mmp) cc_final: 0.7441 (mmt) REVERT: B 443 MET cc_start: 0.8099 (mmp) cc_final: 0.7550 (ttt) REVERT: C 85 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8185 (mt0) REVERT: C 242 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7534 (m-30) REVERT: C 332 ASN cc_start: 0.7682 (t0) cc_final: 0.7479 (t0) REVERT: C 432 GLU cc_start: 0.8507 (tt0) cc_final: 0.8156 (tp30) REVERT: D 119 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8682 (mm) REVERT: D 183 THR cc_start: 0.7477 (p) cc_final: 0.7057 (p) REVERT: D 237 GLU cc_start: 0.7157 (mm-30) cc_final: 0.5844 (tp30) REVERT: D 269 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.6944 (tptt) REVERT: D 401 TYR cc_start: 0.8202 (t80) cc_final: 0.7890 (t80) REVERT: E 49 CYS cc_start: 0.8190 (p) cc_final: 0.7561 (t) REVERT: E 278 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7566 (tt0) REVERT: E 308 ASP cc_start: 0.7970 (m-30) cc_final: 0.7551 (m-30) REVERT: F 107 GLU cc_start: 0.7271 (tt0) cc_final: 0.6861 (tp30) REVERT: F 326 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7913 (tpp) REVERT: F 334 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7403 (mmp80) REVERT: F 411 LEU cc_start: 0.7828 (pt) cc_final: 0.7437 (pp) REVERT: G 1 MET cc_start: 0.2933 (ppp) cc_final: 0.2584 (ppp) REVERT: G 43 ASN cc_start: 0.5409 (t0) cc_final: 0.3448 (p0) REVERT: G 79 PHE cc_start: 0.5643 (m-10) cc_final: 0.5339 (m-10) REVERT: G 87 ASP cc_start: 0.3243 (OUTLIER) cc_final: 0.3027 (m-30) REVERT: G 220 MET cc_start: 0.7731 (mmt) cc_final: 0.7438 (mmt) REVERT: G 221 ASP cc_start: 0.8864 (t70) cc_final: 0.8635 (t0) REVERT: H 927 SER cc_start: 0.8596 (m) cc_final: 0.8230 (t) REVERT: H 2077 GLN cc_start: 0.7492 (pm20) cc_final: 0.7129 (mt0) outliers start: 121 outliers final: 81 residues processed: 480 average time/residue: 0.2993 time to fit residues: 230.2247 Evaluate side-chains 451 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 363 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 229 HIS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 309 MET Chi-restraints excluded: chain H residue 873 MET Chi-restraints excluded: chain H residue 934 ASP Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 938 LEU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 1907 LEU Chi-restraints excluded: chain H residue 1914 LEU Chi-restraints excluded: chain H residue 1999 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 1.9990 chunk 268 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 chunk 247 optimal weight: 0.5980 chunk 137 optimal weight: 0.2980 chunk 24 optimal weight: 0.0970 chunk 98 optimal weight: 0.0020 chunk 156 optimal weight: 4.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- 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** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN F 277 ASN ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 GLN ** H 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 936 HIS ** 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: 0.7161 moved from start: 0.7786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24591 Z= 0.173 Angle : 0.643 15.929 33171 Z= 0.317 Chirality : 0.045 0.356 3885 Planarity : 0.004 0.073 4263 Dihedral : 5.039 51.937 3366 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.69 % Favored : 93.24 % Rotamer: Outliers : 4.53 % Allowed : 20.88 % Favored : 74.59 % 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: -1.07 (0.15), residues: 2988 helix: 0.67 (0.16), residues: 1218 sheet: -0.18 (0.24), residues: 453 loop : -2.31 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 283 HIS 0.007 0.001 HIS G 156 PHE 0.029 0.001 PHE H1978 TYR 0.036 0.001 TYR G 77 ARG 0.004 0.000 ARG B 125 *********************** 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 524 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 405 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7618 (tpp) cc_final: 0.6831 (ttt) REVERT: A 100 GLU cc_start: 0.7460 (tt0) cc_final: 0.7253 (tp30) REVERT: A 124 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8078 (pp) REVERT: A 154 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6700 (tp) REVERT: A 235 ILE cc_start: 0.7321 (mt) cc_final: 0.6897 (pt) REVERT: B 83 LYS cc_start: 0.5220 (OUTLIER) cc_final: 0.3784 (ptpp) REVERT: B 106 SER cc_start: 0.9087 (p) cc_final: 0.8808 (m) REVERT: B 107 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7413 (mp0) REVERT: B 240 HIS cc_start: 0.7295 (OUTLIER) cc_final: 0.5700 (t-90) REVERT: B 443 MET cc_start: 0.8057 (mmp) cc_final: 0.7541 (ttt) REVERT: C 85 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8139 (mt0) REVERT: C 135 VAL cc_start: 0.7348 (OUTLIER) cc_final: 0.7132 (p) REVERT: C 225 LYS cc_start: 0.6758 (mmmt) cc_final: 0.6511 (mmmt) REVERT: C 242 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7376 (m-30) REVERT: C 332 ASN cc_start: 0.7683 (t0) cc_final: 0.7410 (t0) REVERT: C 355 LEU cc_start: 0.9311 (tp) cc_final: 0.8438 (tp) REVERT: C 431 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8178 (pp20) REVERT: C 432 GLU cc_start: 0.8453 (tt0) cc_final: 0.7880 (tp30) REVERT: D 119 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8745 (mm) REVERT: D 269 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6265 (tptt) REVERT: D 303 MET cc_start: 0.7967 (ppp) cc_final: 0.7699 (ppp) REVERT: E 49 CYS cc_start: 0.8143 (p) cc_final: 0.7592 (t) REVERT: E 110 GLU cc_start: 0.7807 (tp30) cc_final: 0.7488 (mm-30) REVERT: E 135 VAL cc_start: 0.7407 (m) cc_final: 0.7190 (p) REVERT: E 278 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7586 (tt0) REVERT: E 308 ASP cc_start: 0.8068 (m-30) cc_final: 0.7767 (m-30) REVERT: E 431 GLU cc_start: 0.9007 (tp30) cc_final: 0.8716 (tp30) REVERT: F 107 GLU cc_start: 0.7322 (tt0) cc_final: 0.6890 (tp30) REVERT: F 326 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7863 (tpp) REVERT: F 334 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7514 (mmp80) REVERT: F 411 LEU cc_start: 0.7852 (pt) cc_final: 0.7495 (pp) REVERT: G 1 MET cc_start: 0.3023 (ppp) cc_final: 0.2599 (ppp) REVERT: G 43 ASN cc_start: 0.5339 (t0) cc_final: 0.3381 (p0) REVERT: G 79 PHE cc_start: 0.5676 (m-10) cc_final: 0.5393 (m-10) REVERT: G 118 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6711 (tm-30) REVERT: G 135 TYR cc_start: 0.8108 (t80) cc_final: 0.7662 (t80) REVERT: G 137 ARG cc_start: 0.3964 (mmm160) cc_final: 0.3427 (mmm160) REVERT: G 220 MET cc_start: 0.7855 (mmt) cc_final: 0.7567 (mmt) REVERT: G 221 ASP cc_start: 0.8770 (t70) cc_final: 0.8531 (t0) REVERT: G 309 MET cc_start: 0.5381 (OUTLIER) cc_final: 0.5080 (mtm) REVERT: H 2007 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7558 (mt0) REVERT: H 2077 GLN cc_start: 0.7375 (pm20) cc_final: 0.7080 (mt0) outliers start: 119 outliers final: 71 residues processed: 481 average time/residue: 0.3158 time to fit residues: 245.1452 Evaluate side-chains 455 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 373 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 229 HIS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 309 MET Chi-restraints excluded: chain H residue 873 MET Chi-restraints excluded: chain H residue 934 ASP Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 938 LEU Chi-restraints excluded: chain H residue 1907 LEU Chi-restraints excluded: chain H residue 1914 LEU Chi-restraints excluded: chain H residue 1999 LEU Chi-restraints excluded: chain H residue 2162 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 217 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 296 optimal weight: 0.0570 chunk 185 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN G 29 GLN ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 323 ASN ** H 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H2027 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.8201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24591 Z= 0.197 Angle : 0.663 15.082 33171 Z= 0.326 Chirality : 0.045 0.324 3885 Planarity : 0.004 0.069 4263 Dihedral : 5.010 54.157 3366 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.20 % Favored : 92.74 % Rotamer: Outliers : 5.02 % Allowed : 21.76 % Favored : 73.22 % 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: -0.93 (0.16), residues: 2988 helix: 0.75 (0.16), residues: 1221 sheet: -0.15 (0.24), residues: 461 loop : -2.20 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H2015 HIS 0.005 0.001 HIS C 316 PHE 0.034 0.001 PHE H1978 TYR 0.033 0.001 TYR G 77 ARG 0.009 0.000 ARG F 235 *********************** 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 521 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 389 time to evaluate : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7613 (tpp) cc_final: 0.7256 (ttt) REVERT: A 100 GLU cc_start: 0.7525 (tt0) cc_final: 0.7314 (tp30) REVERT: A 124 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8112 (pp) REVERT: A 219 GLU cc_start: 0.4964 (pm20) cc_final: 0.4255 (pm20) REVERT: A 235 ILE cc_start: 0.7635 (mt) cc_final: 0.7153 (pt) REVERT: B 83 LYS cc_start: 0.5225 (OUTLIER) cc_final: 0.3711 (ptpp) REVERT: B 106 SER cc_start: 0.9071 (p) cc_final: 0.8840 (m) REVERT: B 107 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7441 (mp0) REVERT: B 169 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8007 (pp20) REVERT: B 240 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.5797 (t-90) REVERT: B 303 MET cc_start: 0.7411 (ppp) cc_final: 0.6835 (ppp) REVERT: B 443 MET cc_start: 0.7975 (mmp) cc_final: 0.7594 (ttt) REVERT: C 85 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8116 (mt0) REVERT: C 225 LYS cc_start: 0.6964 (mmmt) cc_final: 0.6696 (mmmt) REVERT: C 242 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: C 310 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7982 (mt-10) REVERT: C 355 LEU cc_start: 0.9350 (tp) cc_final: 0.8961 (tp) REVERT: C 432 GLU cc_start: 0.8469 (tt0) cc_final: 0.8239 (tp30) REVERT: D 119 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8754 (mm) REVERT: D 237 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6108 (tp30) REVERT: D 269 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6337 (tptt) REVERT: E 49 CYS cc_start: 0.8190 (p) cc_final: 0.7428 (t) REVERT: E 110 GLU cc_start: 0.7857 (tp30) cc_final: 0.7608 (tp30) REVERT: E 278 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7598 (tt0) REVERT: E 308 ASP cc_start: 0.8054 (m-30) cc_final: 0.7568 (m-30) REVERT: E 431 GLU cc_start: 0.9026 (tp30) cc_final: 0.8667 (tp30) REVERT: F 107 GLU cc_start: 0.7366 (tt0) cc_final: 0.6869 (tp30) REVERT: F 285 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7907 (mm-30) REVERT: F 325 ILE cc_start: 0.9100 (mt) cc_final: 0.8780 (mt) REVERT: F 411 LEU cc_start: 0.7906 (pt) cc_final: 0.7564 (pp) REVERT: G 1 MET cc_start: 0.3548 (ppp) cc_final: 0.2984 (ppp) REVERT: G 79 PHE cc_start: 0.5779 (m-10) cc_final: 0.5520 (m-10) REVERT: G 135 TYR cc_start: 0.7948 (t80) cc_final: 0.7586 (t80) REVERT: G 204 GLN cc_start: 0.8625 (tp40) cc_final: 0.7860 (tm-30) REVERT: G 220 MET cc_start: 0.7932 (mmt) cc_final: 0.7632 (mmt) REVERT: G 221 ASP cc_start: 0.8859 (t70) cc_final: 0.8645 (t0) REVERT: G 306 PRO cc_start: 0.7608 (Cg_exo) cc_final: 0.7207 (Cg_endo) REVERT: G 309 MET cc_start: 0.5696 (OUTLIER) cc_final: 0.5227 (mtm) REVERT: G 375 MET cc_start: 0.5600 (pmm) cc_final: 0.3714 (tmm) REVERT: H 2036 ARG cc_start: 0.7183 (ttt-90) cc_final: 0.6391 (tpt170) REVERT: H 2054 GLN cc_start: 0.8094 (tm-30) cc_final: 0.6954 (mt0) REVERT: H 2077 GLN cc_start: 0.7379 (pm20) cc_final: 0.7070 (mt0) outliers start: 132 outliers final: 89 residues processed: 483 average time/residue: 0.3189 time to fit residues: 248.8258 Evaluate side-chains 458 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 362 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 229 HIS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 309 MET Chi-restraints excluded: chain H residue 873 MET Chi-restraints excluded: chain H residue 934 ASP Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 938 LEU Chi-restraints excluded: chain H residue 1907 LEU Chi-restraints excluded: chain H residue 1914 LEU Chi-restraints excluded: chain H residue 1922 VAL Chi-restraints excluded: chain H residue 1999 LEU Chi-restraints excluded: chain H residue 2014 LEU Chi-restraints excluded: chain H residue 2038 ILE Chi-restraints excluded: chain H residue 2162 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 0.0770 chunk 118 optimal weight: 0.9990 chunk 177 optimal weight: 0.5980 chunk 89 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 188 optimal weight: 0.1980 chunk 202 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN G 29 GLN G 118 GLN ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 GLN G 316 ASN ** H 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 936 HIS ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.8416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24591 Z= 0.179 Angle : 0.659 14.746 33171 Z= 0.324 Chirality : 0.045 0.315 3885 Planarity : 0.004 0.062 4263 Dihedral : 4.922 57.906 3366 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.66 % Favored : 93.27 % Rotamer: Outliers : 3.84 % Allowed : 22.97 % Favored : 73.18 % 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: -0.84 (0.16), residues: 2988 helix: 0.81 (0.16), residues: 1222 sheet: -0.02 (0.24), residues: 459 loop : -2.16 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 283 HIS 0.006 0.001 HIS A 316 PHE 0.028 0.002 PHE H1978 TYR 0.035 0.001 TYR G 77 ARG 0.007 0.000 ARG G 137 *********************** 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 478 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 377 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7563 (tpp) cc_final: 0.7220 (ttt) REVERT: A 124 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8187 (pp) REVERT: A 235 ILE cc_start: 0.7600 (mt) cc_final: 0.7090 (pt) REVERT: B 83 LYS cc_start: 0.5090 (OUTLIER) cc_final: 0.3505 (ptpp) REVERT: B 106 SER cc_start: 0.9060 (p) cc_final: 0.8768 (m) REVERT: B 107 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7529 (mp0) REVERT: B 240 HIS cc_start: 0.7433 (OUTLIER) cc_final: 0.5832 (t-90) REVERT: B 443 MET cc_start: 0.7925 (mmp) cc_final: 0.7612 (ttt) REVERT: C 29 SER cc_start: 0.8275 (OUTLIER) cc_final: 0.7674 (t) REVERT: C 242 ASP cc_start: 0.7882 (t0) cc_final: 0.7583 (m-30) REVERT: C 355 LEU cc_start: 0.9325 (tp) cc_final: 0.8427 (tp) REVERT: C 432 GLU cc_start: 0.8516 (tt0) cc_final: 0.8261 (tp30) REVERT: D 119 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8667 (mm) REVERT: D 237 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6132 (tp30) REVERT: D 269 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6305 (tptt) REVERT: D 303 MET cc_start: 0.7932 (ppp) cc_final: 0.7715 (ppp) REVERT: E 49 CYS cc_start: 0.8222 (p) cc_final: 0.7563 (t) REVERT: E 110 GLU cc_start: 0.7890 (tp30) cc_final: 0.7391 (tp30) REVERT: E 278 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7574 (tt0) REVERT: E 359 MET cc_start: 0.8400 (ttt) cc_final: 0.8069 (ttt) REVERT: E 388 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7368 (mm-30) REVERT: E 431 GLU cc_start: 0.9010 (tp30) cc_final: 0.8660 (tp30) REVERT: F 107 GLU cc_start: 0.7440 (tt0) cc_final: 0.6921 (tp30) REVERT: F 113 MET cc_start: 0.7711 (ttm) cc_final: 0.7375 (ttp) REVERT: F 285 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7998 (mm-30) REVERT: F 411 LEU cc_start: 0.7881 (pt) cc_final: 0.7581 (pp) REVERT: G 1 MET cc_start: 0.3515 (ppp) cc_final: 0.2566 (ppp) REVERT: G 25 ILE cc_start: 0.8313 (mm) cc_final: 0.8057 (mp) REVERT: G 79 PHE cc_start: 0.5669 (m-10) cc_final: 0.5426 (m-10) REVERT: G 87 ASP cc_start: 0.3189 (OUTLIER) cc_final: 0.2960 (m-30) REVERT: G 109 MET cc_start: 0.7168 (ptm) cc_final: 0.6954 (ptm) REVERT: G 137 ARG cc_start: 0.4344 (mmm160) cc_final: 0.3800 (mmm160) REVERT: G 204 GLN cc_start: 0.8630 (tp40) cc_final: 0.7892 (tm-30) REVERT: G 220 MET cc_start: 0.7875 (mmt) cc_final: 0.7551 (mmt) REVERT: G 221 ASP cc_start: 0.8796 (t70) cc_final: 0.8595 (t0) REVERT: G 306 PRO cc_start: 0.7760 (Cg_exo) cc_final: 0.7312 (Cg_endo) REVERT: G 309 MET cc_start: 0.5838 (OUTLIER) cc_final: 0.5421 (mtm) REVERT: G 372 PHE cc_start: 0.4679 (m-10) cc_final: 0.4143 (m-10) REVERT: G 375 MET cc_start: 0.5810 (pmm) cc_final: 0.4406 (tmm) REVERT: H 2054 GLN cc_start: 0.8052 (tm-30) cc_final: 0.6946 (mt0) outliers start: 101 outliers final: 75 residues processed: 447 average time/residue: 0.3287 time to fit residues: 233.3609 Evaluate side-chains 432 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 349 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 229 HIS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 309 MET Chi-restraints excluded: chain H residue 938 LEU Chi-restraints excluded: chain H residue 1914 LEU Chi-restraints excluded: chain H residue 1922 VAL Chi-restraints excluded: chain H residue 1999 LEU Chi-restraints excluded: chain H residue 2162 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 1.9990 chunk 284 optimal weight: 0.8980 chunk 259 optimal weight: 0.5980 chunk 276 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 217 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 249 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 414 ASN G 29 GLN ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 ASN ** H 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.8805 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= 0.219 Angle : 0.698 13.866 33171 Z= 0.344 Chirality : 0.045 0.314 3885 Planarity : 0.004 0.058 4263 Dihedral : 4.916 59.697 3360 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.36 % Favored : 92.57 % Rotamer: Outliers : 4.07 % Allowed : 23.32 % Favored : 72.61 % 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: -0.84 (0.16), residues: 2988 helix: 0.80 (0.16), residues: 1218 sheet: 0.02 (0.24), residues: 454 loop : -2.15 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 360 HIS 0.005 0.001 HIS C 20 PHE 0.027 0.002 PHE H1978 TYR 0.033 0.002 TYR G 77 ARG 0.007 0.000 ARG F 235 *********************** 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 478 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 371 time to evaluate : 2.486 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: A 61 MET cc_start: 0.7559 (tpp) cc_final: 0.7186 (ttt) REVERT: A 124 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8226 (pp) REVERT: A 235 ILE cc_start: 0.7908 (mt) cc_final: 0.7415 (pt) REVERT: B 83 LYS cc_start: 0.5328 (OUTLIER) cc_final: 0.3656 (ptpp) REVERT: B 106 SER cc_start: 0.9009 (p) cc_final: 0.8679 (m) REVERT: B 107 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7542 (mp0) REVERT: B 169 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7922 (pp20) REVERT: B 240 HIS cc_start: 0.7494 (OUTLIER) cc_final: 0.5638 (t-90) REVERT: B 387 TYR cc_start: 0.8179 (m-80) cc_final: 0.7872 (m-80) REVERT: C 29 SER cc_start: 0.8365 (OUTLIER) cc_final: 0.7779 (t) REVERT: C 242 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7798 (m-30) REVERT: C 355 LEU cc_start: 0.9345 (tp) cc_final: 0.8944 (tp) REVERT: C 432 GLU cc_start: 0.8535 (tt0) cc_final: 0.8267 (tp30) REVERT: D 119 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8678 (mm) REVERT: D 237 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6324 (tp30) REVERT: D 251 ASN cc_start: 0.7364 (m-40) cc_final: 0.7092 (m-40) REVERT: D 269 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6346 (tptt) REVERT: D 303 MET cc_start: 0.7947 (ppp) cc_final: 0.7708 (ppp) REVERT: D 320 MET cc_start: 0.8866 (mmt) cc_final: 0.8617 (mmt) REVERT: D 405 LEU cc_start: 0.9086 (mt) cc_final: 0.8866 (mt) REVERT: E 49 CYS cc_start: 0.8303 (p) cc_final: 0.7683 (t) REVERT: E 110 GLU cc_start: 0.7904 (tp30) cc_final: 0.7685 (tp30) REVERT: E 278 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7628 (tt0) REVERT: E 302 ASP cc_start: 0.7787 (t0) cc_final: 0.7301 (t0) REVERT: E 429 HIS cc_start: 0.8193 (OUTLIER) cc_final: 0.7942 (t70) REVERT: E 431 GLU cc_start: 0.9040 (tp30) cc_final: 0.8652 (tp30) REVERT: F 107 GLU cc_start: 0.7580 (tt0) cc_final: 0.7255 (tp30) REVERT: F 285 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8093 (mm-30) REVERT: F 411 LEU cc_start: 0.7935 (pt) cc_final: 0.7589 (pp) REVERT: G 1 MET cc_start: 0.3607 (ppp) cc_final: 0.2667 (ppp) REVERT: G 79 PHE cc_start: 0.5762 (m-10) cc_final: 0.5531 (m-10) REVERT: G 87 ASP cc_start: 0.3699 (OUTLIER) cc_final: 0.3494 (m-30) REVERT: G 306 PRO cc_start: 0.7684 (Cg_exo) cc_final: 0.7189 (Cg_endo) REVERT: G 309 MET cc_start: 0.5864 (OUTLIER) cc_final: 0.5480 (mtm) REVERT: G 372 PHE cc_start: 0.4981 (m-10) cc_final: 0.4309 (m-10) REVERT: G 375 MET cc_start: 0.6024 (pmm) cc_final: 0.3649 (tmm) REVERT: H 873 MET cc_start: 0.2037 (OUTLIER) cc_final: -0.2751 (ppp) REVERT: H 936 HIS cc_start: 0.7598 (OUTLIER) cc_final: 0.7050 (p90) REVERT: H 2054 GLN cc_start: 0.8042 (tm-30) cc_final: 0.6910 (mt0) outliers start: 107 outliers final: 78 residues processed: 445 average time/residue: 0.3228 time to fit residues: 229.8360 Evaluate side-chains 440 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 350 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 229 HIS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 309 MET Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain H residue 873 MET Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 938 LEU Chi-restraints excluded: chain H residue 1914 LEU Chi-restraints excluded: chain H residue 1922 VAL Chi-restraints excluded: chain H residue 1999 LEU Chi-restraints excluded: chain H residue 2038 ILE Chi-restraints excluded: chain H residue 2162 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 0.3980 chunk 292 optimal weight: 0.8980 chunk 178 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 203 optimal weight: 1.9990 chunk 306 optimal weight: 4.9990 chunk 282 optimal weight: 0.7980 chunk 244 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 387 HIS H 855 HIS ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.9059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24591 Z= 0.203 Angle : 0.698 13.631 33171 Z= 0.343 Chirality : 0.045 0.317 3885 Planarity : 0.004 0.101 4263 Dihedral : 4.907 57.990 3360 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.73 % Favored : 93.21 % Rotamer: Outliers : 3.92 % Allowed : 23.96 % Favored : 72.12 % 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: -0.77 (0.16), residues: 2988 helix: 0.85 (0.16), residues: 1217 sheet: 0.06 (0.24), residues: 466 loop : -2.11 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 283 HIS 0.006 0.001 HIS E 316 PHE 0.027 0.002 PHE H1978 TYR 0.035 0.002 TYR G 77 ARG 0.008 0.000 ARG F 235 ********************** 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 479 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 376 time to evaluate : 2.840 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: A 49 CYS cc_start: 0.8146 (p) cc_final: 0.7824 (p) REVERT: A 96 MET cc_start: 0.8746 (ptm) cc_final: 0.8525 (ptm) REVERT: A 124 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8256 (pp) REVERT: A 235 ILE cc_start: 0.7908 (mt) cc_final: 0.7413 (pt) REVERT: A 438 TYR cc_start: 0.7144 (OUTLIER) cc_final: 0.6592 (m-10) REVERT: B 83 LYS cc_start: 0.4618 (OUTLIER) cc_final: 0.2916 (ptpp) REVERT: B 106 SER cc_start: 0.9020 (p) cc_final: 0.8601 (m) REVERT: B 107 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7452 (mp0) REVERT: B 169 GLU cc_start: 0.8495 (mt-10) cc_final: 0.7895 (pp20) REVERT: B 180 GLU cc_start: 0.7969 (pp20) cc_final: 0.7239 (mp0) REVERT: B 240 HIS cc_start: 0.7431 (OUTLIER) cc_final: 0.5728 (t-90) REVERT: B 303 MET cc_start: 0.7455 (ppp) cc_final: 0.6882 (tmm) REVERT: C 29 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.7769 (t) REVERT: C 310 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8025 (mt-10) REVERT: C 355 LEU cc_start: 0.9344 (tp) cc_final: 0.8973 (tp) REVERT: C 432 GLU cc_start: 0.8556 (tt0) cc_final: 0.8246 (tp30) REVERT: D 237 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6282 (tp30) REVERT: D 251 ASN cc_start: 0.7326 (m-40) cc_final: 0.7044 (m-40) REVERT: D 269 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6487 (tptt) REVERT: D 303 MET cc_start: 0.7925 (ppp) cc_final: 0.7695 (ppp) REVERT: D 320 MET cc_start: 0.8861 (mmt) cc_final: 0.8615 (mmt) REVERT: D 401 TYR cc_start: 0.7545 (t80) cc_final: 0.7214 (t80) REVERT: D 405 LEU cc_start: 0.9082 (mt) cc_final: 0.8706 (mt) REVERT: E 49 CYS cc_start: 0.8290 (p) cc_final: 0.7672 (t) REVERT: E 278 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7622 (tt0) REVERT: E 429 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.7681 (t-170) REVERT: E 431 GLU cc_start: 0.9013 (tp30) cc_final: 0.8676 (tp30) REVERT: F 169 GLU cc_start: 0.6038 (OUTLIER) cc_final: 0.5441 (tm-30) REVERT: F 285 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8133 (mm-30) REVERT: F 299 ASP cc_start: 0.7765 (t70) cc_final: 0.7515 (t70) REVERT: F 411 LEU cc_start: 0.7913 (pt) cc_final: 0.7570 (pp) REVERT: G 1 MET cc_start: 0.3589 (ppp) cc_final: 0.3033 (ppp) REVERT: G 79 PHE cc_start: 0.5722 (m-10) cc_final: 0.5510 (m-10) REVERT: G 87 ASP cc_start: 0.3306 (OUTLIER) cc_final: 0.3072 (m-30) REVERT: G 306 PRO cc_start: 0.7652 (Cg_exo) cc_final: 0.7160 (Cg_endo) REVERT: G 309 MET cc_start: 0.5835 (OUTLIER) cc_final: 0.5436 (mtm) REVERT: H 936 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.6537 (p90) REVERT: H 1903 ARG cc_start: 0.6845 (mmm-85) cc_final: 0.6625 (mmm-85) REVERT: H 1906 GLN cc_start: 0.8761 (mm110) cc_final: 0.8340 (pp30) REVERT: H 2054 GLN cc_start: 0.7957 (tm-30) cc_final: 0.6843 (mt0) outliers start: 103 outliers final: 80 residues processed: 447 average time/residue: 0.3468 time to fit residues: 247.5306 Evaluate side-chains 445 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 354 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 229 HIS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 309 MET Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain H residue 855 HIS Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 938 LEU Chi-restraints excluded: chain H residue 1914 LEU Chi-restraints excluded: chain H residue 1922 VAL Chi-restraints excluded: chain H residue 1999 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 0.4980 chunk 260 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 225 optimal weight: 0.1980 chunk 36 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 251 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 385 ASN H 855 HIS ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.136468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.116291 restraints weight = 61453.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.118673 restraints weight = 37098.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.120306 restraints weight = 25364.330| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.9226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24591 Z= 0.199 Angle : 0.713 15.099 33171 Z= 0.348 Chirality : 0.046 0.319 3885 Planarity : 0.004 0.067 4263 Dihedral : 4.861 57.712 3360 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.36 % Favored : 92.57 % Rotamer: Outliers : 3.69 % Allowed : 24.76 % Favored : 71.55 % 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: -0.72 (0.16), residues: 2988 helix: 0.89 (0.16), residues: 1221 sheet: 0.12 (0.25), residues: 459 loop : -2.10 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 283 HIS 0.007 0.001 HIS H 855 PHE 0.027 0.001 PHE H1978 TYR 0.035 0.002 TYR G 77 ARG 0.012 0.001 ARG H2002 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5741.55 seconds wall clock time: 103 minutes 49.58 seconds (6229.58 seconds total)