Starting phenix.real_space_refine (version: dev) on Mon Feb 27 04:09:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vak_31845/02_2023/7vak_31845.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vak_31845/02_2023/7vak_31845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vak_31845/02_2023/7vak_31845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vak_31845/02_2023/7vak_31845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vak_31845/02_2023/7vak_31845.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vak_31845/02_2023/7vak_31845.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 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 Process input model Symmetric amino acids flipped Residue "A TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 296": "OE1" <-> "OE2" Residue "E PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 29462 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Time building chain proxies: 15.97, per 1000 atoms: 0.54 Number of scatterers: 29462 At special positions: 0 Unit cell: (149.6, 141.68, 182.16, 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 103 16.00 O 5538 8.00 N 5116 7.00 C 18705 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: 12.89 Conformation dependent library (CDL) restraints added in 4.5 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 28 sheets defined 46.8% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.940A pdb=" N ILE A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.531A pdb=" N PHE A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 4.067A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 298 through 316 Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.591A pdb=" N ARG A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 351 through 352 No H-bonds generated for 'chain 'A' and resid 351 through 352' Processing helix chain 'A' and resid 353 through 364 removed outlier: 3.811A pdb=" N ARG A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.590A pdb=" N ASP A 390 " --> pdb=" O PRO A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 401 Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.999A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 Processing helix chain 'A' and resid 477 through 494 removed outlier: 3.579A pdb=" N VAL A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 531 Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.984A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 558 through 576 removed outlier: 3.509A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 261 through 266 Processing helix chain 'B' and resid 280 through 283 removed outlier: 3.785A pdb=" N HIS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 295 through 317 removed outlier: 5.429A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 342 Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.750A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 463 Processing helix chain 'B' and resid 464 through 472 removed outlier: 3.592A pdb=" N VAL B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 476 Processing helix chain 'B' and resid 477 through 494 Processing helix chain 'B' and resid 508 through 533 removed outlier: 3.723A pdb=" N ALA B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 541 removed outlier: 3.869A pdb=" N ILE B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 550 through 554 removed outlier: 3.603A pdb=" N TYR B 553 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 554 " --> pdb=" O ALA B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 550 through 554' Processing helix chain 'B' and resid 558 through 578 Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.765A pdb=" N ILE C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 259 through 272 Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 317 removed outlier: 4.508A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.503A pdb=" N ALA C 414 " --> pdb=" O ASP C 410 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.314A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 removed outlier: 3.565A pdb=" N LEU C 476 " --> pdb=" O PRO C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 473 through 476' Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 removed outlier: 3.515A pdb=" N ALA C 512 " --> pdb=" O SER C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.838A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.580A pdb=" N ARG C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 554 removed outlier: 3.536A pdb=" N VAL C 554 " --> pdb=" O ALA C 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 551 through 554' Processing helix chain 'C' and resid 558 through 576 removed outlier: 3.524A pdb=" N TYR C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.562A pdb=" N MET D 88 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.609A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.135A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 227 through 250 removed outlier: 3.534A pdb=" N ARG D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 274 removed outlier: 3.566A pdb=" N ARG D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 347 removed outlier: 3.785A pdb=" N HIS D 344 " --> pdb=" O SER D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 374 through 397 removed outlier: 3.608A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 404 removed outlier: 3.541A pdb=" N LEU D 404 " --> pdb=" O GLU D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 removed outlier: 3.594A pdb=" N ARG D 409 " --> pdb=" O THR D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 468 through 473 removed outlier: 3.590A pdb=" N GLY D 472 " --> pdb=" O GLU D 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.713A pdb=" N MET E 88 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 89' Processing helix chain 'E' and resid 120 through 124 removed outlier: 3.685A pdb=" N ARG E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 141 Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.670A pdb=" N ILE E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 212 removed outlier: 3.566A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 229 through 250 removed outlier: 3.837A pdb=" N LEU E 233 " --> pdb=" O ILE E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.952A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA E 273 " --> pdb=" O GLU E 269 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 333 removed outlier: 3.822A pdb=" N ILE E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 347 Processing helix chain 'E' and resid 361 through 366 removed outlier: 3.870A pdb=" N GLY E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 397 removed outlier: 3.614A pdb=" N VAL E 378 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN E 388 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY E 389 " --> pdb=" O ALA E 385 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL E 390 " --> pdb=" O TYR E 386 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 422 removed outlier: 3.717A pdb=" N ARG E 409 " --> pdb=" O THR E 405 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 445 removed outlier: 3.541A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 463 removed outlier: 3.707A pdb=" N ILE E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY E 460 " --> pdb=" O LYS E 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 174 through 178 Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 213 through 217 removed outlier: 3.564A pdb=" N SER F 217 " --> pdb=" O LEU F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 260 through 275 Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.708A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU F 296 " --> pdb=" O ALA F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 362 through 366 removed outlier: 3.933A pdb=" N VAL F 366 " --> pdb=" O ASN F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.996A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 470 Processing helix chain 'G' and resid 7 through 70 removed outlier: 3.911A pdb=" N LEU G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS G 58 " --> pdb=" O ASP G 54 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU G 59 " --> pdb=" O GLN G 55 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE G 70 " --> pdb=" O LEU G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 83 Processing helix chain 'G' and resid 122 through 209 removed outlier: 3.577A pdb=" N ARG G 131 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 6 through 16 removed outlier: 4.225A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.986A pdb=" N GLU H 34 " --> pdb=" O GLN H 30 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR H 35 " --> pdb=" O SER H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 63 removed outlier: 4.807A pdb=" N ARG H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 83 Processing helix chain 'H' and resid 85 through 99 Processing helix chain 'I' and resid 82 through 105 removed outlier: 4.077A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 removed outlier: 3.728A pdb=" N LEU I 119 " --> pdb=" O LEU I 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 92 removed outlier: 3.895A pdb=" N LEU J 66 " --> pdb=" O SER J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 97 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.663A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 131 removed outlier: 3.531A pdb=" N LEU J 128 " --> pdb=" O PRO J 125 " (cutoff:3.500A) Proline residue: J 129 - end of helix Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.475A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 105 removed outlier: 3.749A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 119 Processing helix chain 'L' and resid 62 through 93 Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 124 through 126 No H-bonds generated for 'chain 'L' and resid 124 through 126' Processing helix chain 'L' and resid 127 through 139 removed outlier: 3.893A pdb=" N LEU L 131 " --> pdb=" O ASP L 127 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 5.057A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.512A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 7.011A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 47 through 51 current: chain 'B' and resid 35 through 43 removed outlier: 6.771A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.726A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C 43 " --> pdb=" O THR C 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 6.656A pdb=" N VAL D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 22 current: chain 'E' and resid 42 through 51 removed outlier: 7.084A pdb=" N VAL E 56 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL E 50 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYR E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 54 through 59 current: chain 'F' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 22 current: chain 'F' and resid 42 through 51 removed outlier: 5.774A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR F 54 " --> pdb=" O SER F 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 54 through 59 current: chain 'J' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 151 through 155 removed outlier: 3.517A pdb=" N VAL L 152 " --> pdb=" O ASN L 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 removed outlier: 3.575A pdb=" N TRP A 187 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 84 current: chain 'A' and resid 285 through 288 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 288 current: chain 'A' and resid 375 through 382 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 382 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 119 removed outlier: 3.505A pdb=" N TRP A 117 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 164 " --> pdb=" O TRP A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 3.588A pdb=" N GLY A 155 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 134 through 140 removed outlier: 4.040A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA8, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.506A pdb=" N TRP B 187 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 82 through 84 current: chain 'B' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 291 current: chain 'B' and resid 375 through 383 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 383 current: chain 'B' and resid 422 through 429 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 129 removed outlier: 6.961A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL B 160 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL B 172 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 173 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 134 through 140 removed outlier: 3.666A pdb=" N PHE B 143 " --> pdb=" O GLU B 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.653A pdb=" N VAL C 73 " --> pdb=" O TRP C 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP C 187 " --> pdb=" O VAL C 73 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 84 current: chain 'C' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 291 current: chain 'C' and resid 375 through 383 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 117 through 118 removed outlier: 3.595A pdb=" N TYR C 166 " --> pdb=" O TRP C 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.994A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 128 through 129 removed outlier: 4.011A pdb=" N GLY C 155 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL C 173 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 405 through 406 Processing sheet with id=AB9, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.927A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 92 through 93 removed outlier: 3.604A pdb=" N VAL D 190 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL D 253 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE D 311 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL D 255 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE D 313 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU D 257 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N SER D 315 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.546A pdb=" N LEU E 112 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 92 through 93 removed outlier: 6.189A pdb=" N PHE E 93 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LYS E 223 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA E 188 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 257 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.483A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 152 through 154 removed outlier: 5.908A pdb=" N ILE E 152 " --> pdb=" O LEU E 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 335 through 336 Processing sheet with id=AC7, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC8, first strand: chain 'F' and resid 92 through 93 removed outlier: 6.860A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 314 " --> pdb=" O ILE F 152 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 91 through 96 Processing sheet with id=AD1, first strand: chain 'H' and resid 19 through 21 removed outlier: 3.650A pdb=" N TYR H 21 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA H 2 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA H 46 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL H 45 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1244 hydrogen bonds defined for protein. 3594 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: 9.90 Time building geometry restraints manager: 13.25 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: 9944 1.34 - 1.46: 4173 1.46 - 1.57: 15704 1.57 - 1.69: 0 1.69 - 1.81: 194 Bond restraints: 30015 Sorted by residual: bond pdb=" C HIS C 418 " pdb=" N PHE C 419 " ideal model delta sigma weight residual 1.331 1.313 0.017 1.48e-02 4.57e+03 1.37e+00 bond pdb=" CG PRO A 420 " pdb=" CD PRO A 420 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.23e+00 bond pdb=" N LEU F 355 " pdb=" CA LEU F 355 " ideal model delta sigma weight residual 1.463 1.457 0.006 6.90e-03 2.10e+04 7.93e-01 bond pdb=" C HIS A 418 " pdb=" N PHE A 419 " ideal model delta sigma weight residual 1.331 1.307 0.024 2.83e-02 1.25e+03 7.49e-01 bond pdb=" CG GLU K 117 " pdb=" CD GLU K 117 " ideal model delta sigma weight residual 1.516 1.494 0.022 2.50e-02 1.60e+03 7.40e-01 ... (remaining 30010 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.03: 869 106.03 - 113.04: 15979 113.04 - 120.05: 10748 120.05 - 127.06: 12761 127.06 - 134.07: 301 Bond angle restraints: 40658 Sorted by residual: angle pdb=" C HIS C 418 " pdb=" N PHE C 419 " pdb=" CA PHE C 419 " ideal model delta sigma weight residual 121.03 115.14 5.89 1.60e+00 3.91e-01 1.36e+01 angle pdb=" CA LEU L 148 " pdb=" CB LEU L 148 " pdb=" CG LEU L 148 " ideal model delta sigma weight residual 116.30 127.66 -11.36 3.50e+00 8.16e-02 1.05e+01 angle pdb=" C ILE E 352 " pdb=" N ASP E 353 " pdb=" CA ASP E 353 " ideal model delta sigma weight residual 120.97 111.77 9.20 2.84e+00 1.24e-01 1.05e+01 angle pdb=" CA LEU H 32 " pdb=" CB LEU H 32 " pdb=" CG LEU H 32 " ideal model delta sigma weight residual 116.30 126.83 -10.53 3.50e+00 8.16e-02 9.05e+00 angle pdb=" C MET B 19 " pdb=" N LEU B 20 " pdb=" CA LEU B 20 " ideal model delta sigma weight residual 120.82 125.28 -4.46 1.50e+00 4.44e-01 8.83e+00 ... (remaining 40653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 16660 17.76 - 35.52: 1373 35.52 - 53.29: 203 53.29 - 71.05: 48 71.05 - 88.81: 20 Dihedral angle restraints: 18304 sinusoidal: 7482 harmonic: 10822 Sorted by residual: dihedral pdb=" CA ARG K 87 " pdb=" C ARG K 87 " pdb=" N TYR K 88 " pdb=" CA TYR K 88 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA VAL G 167 " pdb=" C VAL G 167 " pdb=" N VAL G 168 " pdb=" CA VAL G 168 " ideal model delta harmonic sigma weight residual -180.00 -162.88 -17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASP E 290 " pdb=" CB ASP E 290 " pdb=" CG ASP E 290 " pdb=" OD1 ASP E 290 " ideal model delta sinusoidal sigma weight residual -30.00 -86.84 56.84 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3032 0.035 - 0.070: 989 0.070 - 0.104: 405 0.104 - 0.139: 126 0.139 - 0.174: 8 Chirality restraints: 4560 Sorted by residual: chirality pdb=" CA ILE B 15 " pdb=" N ILE B 15 " pdb=" C ILE B 15 " pdb=" CB ILE B 15 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA ARG K 87 " pdb=" N ARG K 87 " pdb=" C ARG K 87 " pdb=" CB ARG K 87 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 4557 not shown) Planarity restraints: 5330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO E 324 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO B 229 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 161 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO B 162 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " -0.023 5.00e-02 4.00e+02 ... (remaining 5327 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 514 2.67 - 3.23: 28745 3.23 - 3.79: 45630 3.79 - 4.34: 60164 4.34 - 4.90: 99895 Nonbonded interactions: 234948 Sorted by model distance: nonbonded pdb=" OG1 THR E 405 " pdb=" OD1 ASN E 407 " model vdw 2.115 2.440 nonbonded pdb=" OG SER B 535 " pdb=" OD1 ASP B 537 " model vdw 2.127 2.440 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.162 2.440 nonbonded pdb=" OH TYR D 411 " pdb=" OE1 GLU D 450 " model vdw 2.167 2.440 nonbonded pdb=" O ARG C 547 " pdb=" OH TYR C 562 " model vdw 2.173 2.440 ... (remaining 234943 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 103 5.16 5 C 18705 2.51 5 N 5116 2.21 5 O 5538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 22.150 Check model and map are aligned: 0.420 Process input model: 73.470 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.270 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 30015 Z= 0.176 Angle : 0.546 11.365 40658 Z= 0.287 Chirality : 0.043 0.174 4560 Planarity : 0.004 0.053 5330 Dihedral : 13.320 88.809 11386 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.14), residues: 3764 helix: 1.42 (0.14), residues: 1533 sheet: -0.16 (0.23), residues: 545 loop : -0.57 (0.16), residues: 1686 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 663 time to evaluate : 3.767 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 outliers start: 0 outliers final: 0 residues processed: 663 average time/residue: 0.5157 time to fit residues: 504.5539 Evaluate side-chains 259 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 3.682 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 9.9990 chunk 282 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 292 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 338 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 GLN E 262 ASN E 388 ASN F 142 ASN F 437 GLN F 458 HIS G 162 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 30015 Z= 0.427 Angle : 0.738 13.391 40658 Z= 0.376 Chirality : 0.048 0.190 4560 Planarity : 0.006 0.064 5330 Dihedral : 4.791 22.827 4180 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3764 helix: 0.85 (0.13), residues: 1549 sheet: -0.29 (0.23), residues: 554 loop : -0.90 (0.15), residues: 1661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 313 time to evaluate : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 318 average time/residue: 0.4332 time to fit residues: 218.0736 Evaluate side-chains 202 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 198 time to evaluate : 3.525 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2637 time to fit residues: 7.0241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 230 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 339 optimal weight: 9.9990 chunk 366 optimal weight: 10.0000 chunk 302 optimal weight: 7.9990 chunk 336 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN B 239 GLN B 397 GLN B 442 ASN C 290 ASN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN J 130 HIS ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 30015 Z= 0.395 Angle : 0.689 13.653 40658 Z= 0.353 Chirality : 0.048 0.217 4560 Planarity : 0.006 0.082 5330 Dihedral : 4.916 32.964 4180 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3764 helix: 0.78 (0.13), residues: 1553 sheet: -0.49 (0.23), residues: 536 loop : -1.05 (0.15), residues: 1675 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 277 time to evaluate : 3.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 280 average time/residue: 0.4631 time to fit residues: 206.0183 Evaluate side-chains 193 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 3.441 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2908 time to fit residues: 5.8644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 227 optimal weight: 8.9990 chunk 340 optimal weight: 10.0000 chunk 360 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 322 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN B 239 GLN B 397 GLN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 68 GLN J 130 HIS ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.057 30015 Z= 0.562 Angle : 0.842 14.922 40658 Z= 0.431 Chirality : 0.052 0.210 4560 Planarity : 0.007 0.073 5330 Dihedral : 5.511 23.306 4180 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 3764 helix: 0.29 (0.13), residues: 1535 sheet: -0.78 (0.22), residues: 547 loop : -1.41 (0.15), residues: 1682 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 255 time to evaluate : 3.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 258 average time/residue: 0.4407 time to fit residues: 183.1264 Evaluate side-chains 179 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 176 time to evaluate : 3.589 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2659 time to fit residues: 6.1916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 307 optimal weight: 0.9980 chunk 249 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 323 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS A 469 GLN B 239 GLN B 571 GLN C 316 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN J 130 HIS L 165 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 30015 Z= 0.187 Angle : 0.583 11.241 40658 Z= 0.297 Chirality : 0.045 0.214 4560 Planarity : 0.005 0.069 5330 Dihedral : 4.704 22.609 4180 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3764 helix: 0.93 (0.13), residues: 1550 sheet: -0.60 (0.23), residues: 527 loop : -1.15 (0.15), residues: 1687 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 297 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 297 average time/residue: 0.4332 time to fit residues: 207.6261 Evaluate side-chains 182 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 3.642 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 8.9990 chunk 324 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 360 optimal weight: 0.9990 chunk 299 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 442 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 30015 Z= 0.404 Angle : 0.700 12.586 40658 Z= 0.358 Chirality : 0.048 0.193 4560 Planarity : 0.006 0.060 5330 Dihedral : 5.009 22.079 4180 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3764 helix: 0.73 (0.13), residues: 1545 sheet: -0.60 (0.23), residues: 513 loop : -1.29 (0.15), residues: 1706 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 3.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.4280 time to fit residues: 177.9047 Evaluate side-chains 173 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 3.518 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 205 optimal weight: 0.9980 chunk 263 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 303 optimal weight: 8.9990 chunk 201 optimal weight: 0.7980 chunk 359 optimal weight: 6.9990 chunk 224 optimal weight: 0.5980 chunk 219 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 30015 Z= 0.170 Angle : 0.570 10.191 40658 Z= 0.289 Chirality : 0.044 0.253 4560 Planarity : 0.004 0.052 5330 Dihedral : 4.539 22.468 4180 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3764 helix: 1.11 (0.14), residues: 1541 sheet: -0.65 (0.22), residues: 546 loop : -1.03 (0.15), residues: 1677 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 3.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.4374 time to fit residues: 193.4115 Evaluate side-chains 175 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 3.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 69 optimal weight: 0.3980 chunk 228 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 282 optimal weight: 9.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 30015 Z= 0.259 Angle : 0.605 11.203 40658 Z= 0.306 Chirality : 0.045 0.234 4560 Planarity : 0.005 0.051 5330 Dihedral : 4.560 21.162 4180 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3764 helix: 1.13 (0.13), residues: 1539 sheet: -0.71 (0.22), residues: 562 loop : -1.07 (0.15), residues: 1663 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.4218 time to fit residues: 167.9419 Evaluate side-chains 169 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 3.328 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 4.9990 chunk 344 optimal weight: 7.9990 chunk 314 optimal weight: 9.9990 chunk 335 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 263 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 302 optimal weight: 9.9990 chunk 316 optimal weight: 7.9990 chunk 333 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN C 316 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 30015 Z= 0.394 Angle : 0.704 12.594 40658 Z= 0.360 Chirality : 0.048 0.264 4560 Planarity : 0.006 0.077 5330 Dihedral : 4.966 22.140 4180 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3764 helix: 0.78 (0.13), residues: 1547 sheet: -0.69 (0.23), residues: 509 loop : -1.24 (0.15), residues: 1708 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 3.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 245 average time/residue: 0.4137 time to fit residues: 167.3992 Evaluate side-chains 172 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 3.310 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 0.0670 chunk 354 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 246 optimal weight: 0.9990 chunk 371 optimal weight: 8.9990 chunk 342 optimal weight: 10.0000 chunk 295 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 228 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN B 81 ASN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 HIS ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 30015 Z= 0.162 Angle : 0.591 11.445 40658 Z= 0.297 Chirality : 0.044 0.213 4560 Planarity : 0.004 0.068 5330 Dihedral : 4.437 26.851 4180 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3764 helix: 1.16 (0.14), residues: 1549 sheet: -0.54 (0.23), residues: 547 loop : -1.04 (0.15), residues: 1668 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 3.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.4462 time to fit residues: 190.3552 Evaluate side-chains 184 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 3.947 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 0.5980 chunk 315 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 82 optimal weight: 0.0980 chunk 296 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 304 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.062976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.051461 restraints weight = 119782.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.052529 restraints weight = 77460.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.053283 restraints weight = 55339.075| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 30015 Z= 0.231 Angle : 0.609 11.917 40658 Z= 0.308 Chirality : 0.045 0.214 4560 Planarity : 0.005 0.061 5330 Dihedral : 4.446 22.725 4180 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3764 helix: 1.16 (0.14), residues: 1549 sheet: -0.54 (0.23), residues: 525 loop : -1.05 (0.15), residues: 1690 =============================================================================== Job complete usr+sys time: 5016.28 seconds wall clock time: 93 minutes 35.91 seconds (5615.91 seconds total)