Starting phenix.real_space_refine on Wed Feb 21 01:56:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vak_31845/02_2024/7vak_31845.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vak_31845/02_2024/7vak_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_2024/7vak_31845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vak_31845/02_2024/7vak_31845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vak_31845/02_2024/7vak_31845.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vak_31845/02_2024/7vak_31845.pdb" } resolution = 4.7 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= 0.003 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 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. 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-5238/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: 15.43, per 1000 atoms: 0.52 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: 12.82 Conformation dependent library (CDL) restraints added in 5.7 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: 3.36 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: 10.39 Time building geometry restraints manager: 13.67 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 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: 5.120 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: 20.580 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 78.590 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.190 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 % Allowed : 0.19 % Favored : 99.81 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 100 HIS 0.007 0.001 HIS E 458 PHE 0.021 0.001 PHE A 269 TYR 0.011 0.001 TYR D 331 ARG 0.003 0.000 ARG B 532 *********************** 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 : 3.509 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: A 106 VAL cc_start: 0.8493 (t) cc_final: 0.8173 (m) REVERT: A 133 MET cc_start: 0.7337 (mtp) cc_final: 0.6781 (mmm) REVERT: A 152 ASP cc_start: 0.8234 (m-30) cc_final: 0.7710 (p0) REVERT: A 153 VAL cc_start: 0.8739 (t) cc_final: 0.8353 (m) REVERT: A 169 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7410 (mt-10) REVERT: A 175 LEU cc_start: 0.8084 (mt) cc_final: 0.7430 (tp) REVERT: A 179 THR cc_start: 0.8103 (m) cc_final: 0.7803 (p) REVERT: A 220 MET cc_start: 0.7902 (tpp) cc_final: 0.7477 (ttp) REVERT: A 239 GLN cc_start: 0.7643 (mt0) cc_final: 0.7384 (pt0) REVERT: A 262 MET cc_start: 0.6702 (mmt) cc_final: 0.6446 (mmt) REVERT: A 323 MET cc_start: 0.7384 (mmt) cc_final: 0.7109 (mmt) REVERT: A 498 ASN cc_start: 0.8164 (t0) cc_final: 0.7471 (t0) REVERT: B 133 MET cc_start: 0.6876 (mtp) cc_final: 0.6632 (tmm) REVERT: B 186 THR cc_start: 0.8384 (p) cc_final: 0.7952 (t) REVERT: B 264 ASP cc_start: 0.7597 (p0) cc_final: 0.7250 (t70) REVERT: B 344 MET cc_start: 0.8411 (ptp) cc_final: 0.7893 (ppp) REVERT: C 161 LYS cc_start: 0.7433 (mmtm) cc_final: 0.6777 (mmtp) REVERT: C 170 GLU cc_start: 0.8129 (tp30) cc_final: 0.7849 (tm-30) REVERT: C 183 MET cc_start: 0.8957 (mtt) cc_final: 0.8391 (mtp) REVERT: C 212 LEU cc_start: 0.7872 (mt) cc_final: 0.7623 (mt) REVERT: C 282 MET cc_start: 0.7982 (tpt) cc_final: 0.7533 (tpt) REVERT: C 427 SER cc_start: 0.8025 (m) cc_final: 0.7812 (t) REVERT: C 520 LEU cc_start: 0.8142 (mt) cc_final: 0.7893 (tt) REVERT: C 546 GLU cc_start: 0.7830 (mp0) cc_final: 0.7534 (tm-30) REVERT: C 548 ILE cc_start: 0.8752 (mt) cc_final: 0.8505 (mt) REVERT: D 142 ASN cc_start: 0.8778 (m-40) cc_final: 0.8539 (m110) REVERT: D 190 VAL cc_start: 0.8352 (t) cc_final: 0.7931 (p) REVERT: D 230 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8016 (mt-10) REVERT: D 253 VAL cc_start: 0.9013 (t) cc_final: 0.8715 (m) REVERT: D 259 ASP cc_start: 0.6759 (t0) cc_final: 0.6508 (t0) REVERT: D 260 MET cc_start: 0.8594 (mmm) cc_final: 0.8034 (mmm) REVERT: D 276 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7302 (pt0) REVERT: D 305 LYS cc_start: 0.8401 (mtmt) cc_final: 0.8049 (tttm) REVERT: E 106 ILE cc_start: 0.6133 (pt) cc_final: 0.5754 (pt) REVERT: E 214 LEU cc_start: 0.7675 (mt) cc_final: 0.7161 (mt) REVERT: E 296 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7816 (tp30) REVERT: E 360 ARG cc_start: 0.7166 (mtt180) cc_final: 0.6901 (mtp180) REVERT: E 401 GLU cc_start: 0.8274 (pp20) cc_final: 0.7943 (mp0) REVERT: E 420 ARG cc_start: 0.8842 (mtp180) cc_final: 0.8062 (tpp-160) REVERT: F 4 LEU cc_start: 0.7227 (pt) cc_final: 0.6922 (tt) REVERT: F 11 ILE cc_start: 0.8857 (mm) cc_final: 0.8624 (mp) REVERT: F 35 ILE cc_start: 0.8621 (mt) cc_final: 0.8316 (mt) REVERT: F 88 MET cc_start: 0.7624 (ptm) cc_final: 0.7254 (ptm) REVERT: F 89 LEU cc_start: 0.7631 (mt) cc_final: 0.7177 (tp) REVERT: F 194 MET cc_start: 0.8032 (mtm) cc_final: 0.7753 (mpp) REVERT: F 269 GLU cc_start: 0.8667 (tt0) cc_final: 0.8097 (tt0) REVERT: F 275 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7420 (pt0) REVERT: F 327 ASP cc_start: 0.7956 (t0) cc_final: 0.7751 (t0) REVERT: F 349 TYR cc_start: 0.8032 (t80) cc_final: 0.7783 (t80) REVERT: G 145 THR cc_start: 0.8478 (t) cc_final: 0.8148 (p) REVERT: H 36 LEU cc_start: 0.6286 (tp) cc_final: 0.5840 (mm) REVERT: H 39 ARG cc_start: 0.6418 (ttp80) cc_final: 0.6186 (tmt170) REVERT: H 52 LEU cc_start: 0.5293 (pt) cc_final: 0.5071 (mp) REVERT: H 68 LEU cc_start: 0.4985 (tp) cc_final: 0.4731 (mm) REVERT: J 78 GLU cc_start: 0.7781 (tp30) cc_final: 0.7442 (mt-10) REVERT: J 84 ARG cc_start: 0.6172 (mtt180) cc_final: 0.5945 (ttp-110) REVERT: J 99 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6993 (pm20) REVERT: J 115 LEU cc_start: 0.5660 (mt) cc_final: 0.5457 (mt) REVERT: J 126 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7156 (mp0) REVERT: J 134 LEU cc_start: 0.6754 (mm) cc_final: 0.6462 (mt) REVERT: L 78 GLU cc_start: 0.7157 (tt0) cc_final: 0.6923 (mm-30) REVERT: L 88 ARG cc_start: 0.7107 (mtp-110) cc_final: 0.6530 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 663 average time/residue: 0.4955 time to fit residues: 485.6979 Evaluate side-chains 288 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 3.531 ------------------------------------------------------------------------------- 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: 3.9990 chunk 156 optimal weight: 9.9990 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: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN C 290 ASN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN 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: 0.7458 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 30015 Z= 0.386 Angle : 0.688 12.566 40658 Z= 0.351 Chirality : 0.047 0.232 4560 Planarity : 0.005 0.061 5330 Dihedral : 4.603 18.922 4180 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.19 % Allowed : 5.51 % Favored : 94.29 % 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: -0.01 (0.14), residues: 3764 helix: 0.99 (0.13), residues: 1558 sheet: -0.18 (0.23), residues: 539 loop : -0.86 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 100 HIS 0.009 0.002 HIS F 249 PHE 0.042 0.002 PHE A 269 TYR 0.020 0.002 TYR F 463 ARG 0.024 0.001 ARG E 430 *********************** 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 341 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 335 time to evaluate : 3.627 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 24 MET cc_start: 0.8416 (mmm) cc_final: 0.7570 (tpp) REVERT: A 133 MET cc_start: 0.7587 (mtp) cc_final: 0.7060 (mmm) REVERT: A 169 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7380 (mt-10) REVERT: A 175 LEU cc_start: 0.8327 (mt) cc_final: 0.7579 (tp) REVERT: A 179 THR cc_start: 0.8436 (m) cc_final: 0.8079 (p) REVERT: A 220 MET cc_start: 0.7942 (tpp) cc_final: 0.7366 (ttp) REVERT: A 239 GLN cc_start: 0.7673 (mt0) cc_final: 0.7430 (tt0) REVERT: A 282 MET cc_start: 0.8160 (mmp) cc_final: 0.7905 (mmm) REVERT: A 330 TRP cc_start: 0.8235 (t60) cc_final: 0.7599 (t-100) REVERT: A 498 ASN cc_start: 0.8289 (t0) cc_final: 0.7654 (t0) REVERT: A 550 ARG cc_start: 0.7428 (tpp-160) cc_final: 0.6896 (mmm160) REVERT: B 133 MET cc_start: 0.7643 (mtp) cc_final: 0.7314 (tmm) REVERT: B 209 MET cc_start: 0.7061 (mtm) cc_final: 0.6774 (mtp) REVERT: B 262 MET cc_start: 0.8848 (pmm) cc_final: 0.8631 (pmm) REVERT: B 282 MET cc_start: 0.8551 (tpt) cc_final: 0.8012 (tpp) REVERT: C 24 MET cc_start: 0.8521 (mtp) cc_final: 0.8315 (mtp) REVERT: C 38 GLU cc_start: 0.7983 (tt0) cc_final: 0.7692 (tt0) REVERT: C 161 LYS cc_start: 0.7381 (mmtm) cc_final: 0.6966 (mmtt) REVERT: C 183 MET cc_start: 0.8823 (mtt) cc_final: 0.8247 (mtp) REVERT: C 282 MET cc_start: 0.7904 (tpt) cc_final: 0.7341 (tpt) REVERT: C 294 MET cc_start: 0.8347 (mtt) cc_final: 0.8038 (mtt) REVERT: C 498 ASN cc_start: 0.8513 (m-40) cc_final: 0.8189 (m-40) REVERT: C 520 LEU cc_start: 0.8117 (mt) cc_final: 0.7768 (tt) REVERT: D 190 VAL cc_start: 0.7956 (t) cc_final: 0.7609 (p) REVERT: D 194 MET cc_start: 0.7634 (mtp) cc_final: 0.7317 (mtp) REVERT: D 230 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8111 (mt-10) REVERT: D 237 MET cc_start: 0.8928 (mmm) cc_final: 0.8713 (mmm) REVERT: D 260 MET cc_start: 0.8777 (mmm) cc_final: 0.8470 (mmm) REVERT: D 276 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7423 (pt0) REVERT: D 305 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8117 (tttp) REVERT: D 420 ARG cc_start: 0.6991 (mtp-110) cc_final: 0.6777 (mtp-110) REVERT: E 214 LEU cc_start: 0.7754 (mt) cc_final: 0.7544 (mt) REVERT: E 296 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7653 (tp30) REVERT: E 360 ARG cc_start: 0.7089 (mtt180) cc_final: 0.6867 (mtp180) REVERT: E 401 GLU cc_start: 0.8301 (pp20) cc_final: 0.8078 (mp0) REVERT: E 411 TYR cc_start: 0.6371 (m-80) cc_final: 0.6111 (m-80) REVERT: E 420 ARG cc_start: 0.8776 (mtp180) cc_final: 0.8269 (tpp-160) REVERT: E 462 TYR cc_start: 0.6042 (m-80) cc_final: 0.5783 (m-10) REVERT: F 11 ILE cc_start: 0.9035 (mm) cc_final: 0.8824 (mp) REVERT: F 88 MET cc_start: 0.7738 (ptm) cc_final: 0.7400 (ptm) REVERT: F 89 LEU cc_start: 0.8182 (mt) cc_final: 0.7799 (tp) REVERT: F 194 MET cc_start: 0.8279 (mtm) cc_final: 0.8031 (mpp) REVERT: F 269 GLU cc_start: 0.8782 (tt0) cc_final: 0.8363 (tt0) REVERT: F 349 TYR cc_start: 0.8180 (t80) cc_final: 0.7945 (t80) REVERT: H 39 ARG cc_start: 0.6573 (ttp80) cc_final: 0.6194 (tmt170) REVERT: I 104 MET cc_start: 0.7319 (ttp) cc_final: 0.7105 (ttp) REVERT: J 78 GLU cc_start: 0.7736 (tp30) cc_final: 0.7425 (mt-10) REVERT: J 99 GLU cc_start: 0.7171 (tm-30) cc_final: 0.6912 (pm20) REVERT: J 126 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7310 (mp0) REVERT: K 91 ARG cc_start: 0.5958 (mtm-85) cc_final: 0.5458 (mtm-85) outliers start: 6 outliers final: 4 residues processed: 341 average time/residue: 0.4406 time to fit residues: 236.4725 Evaluate side-chains 231 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 227 time to evaluate : 3.747 ------------------------------------------------------------------------------- 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: 10.0000 chunk 105 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 339 optimal weight: 9.9990 chunk 366 optimal weight: 10.0000 chunk 302 optimal weight: 1.9990 chunk 336 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 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 442 ASN C 290 ASN ** 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** D 338 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 30015 Z= 0.424 Angle : 0.698 13.674 40658 Z= 0.358 Chirality : 0.048 0.214 4560 Planarity : 0.006 0.063 5330 Dihedral : 4.887 25.208 4180 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.81 % Favored : 95.16 % Rotamer: Outliers : 0.06 % Allowed : 5.64 % Favored : 94.29 % 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: -0.30 (0.14), residues: 3764 helix: 0.79 (0.13), residues: 1556 sheet: -0.46 (0.23), residues: 543 loop : -1.01 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 100 HIS 0.016 0.002 HIS D 375 PHE 0.026 0.002 PHE G 40 TYR 0.023 0.002 TYR F 463 ARG 0.007 0.001 ARG L 88 *********************** 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 297 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 295 time to evaluate : 3.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.7904 (mtp) cc_final: 0.7138 (mmm) REVERT: A 175 LEU cc_start: 0.8278 (mt) cc_final: 0.7556 (tp) REVERT: A 179 THR cc_start: 0.8425 (m) cc_final: 0.8147 (p) REVERT: A 220 MET cc_start: 0.7865 (tpp) cc_final: 0.7398 (ttp) REVERT: A 282 MET cc_start: 0.8232 (mmp) cc_final: 0.7769 (mmm) REVERT: A 498 ASN cc_start: 0.8383 (t0) cc_final: 0.7831 (t0) REVERT: A 550 ARG cc_start: 0.7380 (tpp-160) cc_final: 0.6765 (mmm160) REVERT: B 133 MET cc_start: 0.7858 (mtp) cc_final: 0.7330 (tmm) REVERT: B 262 MET cc_start: 0.8938 (pmm) cc_final: 0.8503 (pmm) REVERT: B 282 MET cc_start: 0.8745 (tpt) cc_final: 0.8129 (tpp) REVERT: C 114 GLU cc_start: 0.8088 (mp0) cc_final: 0.7495 (pm20) REVERT: C 161 LYS cc_start: 0.7680 (mmtm) cc_final: 0.7294 (mmtt) REVERT: C 183 MET cc_start: 0.8714 (mtt) cc_final: 0.8105 (mtp) REVERT: C 282 MET cc_start: 0.7950 (tpt) cc_final: 0.7446 (tpt) REVERT: C 441 GLU cc_start: 0.8182 (mp0) cc_final: 0.7939 (tm-30) REVERT: C 520 LEU cc_start: 0.8177 (mt) cc_final: 0.7791 (tt) REVERT: C 556 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7872 (tp30) REVERT: D 142 ASN cc_start: 0.8337 (m110) cc_final: 0.8084 (m110) REVERT: D 190 VAL cc_start: 0.7942 (t) cc_final: 0.7619 (p) REVERT: D 230 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8016 (mt-10) REVERT: D 259 ASP cc_start: 0.7249 (t0) cc_final: 0.6991 (t0) REVERT: D 260 MET cc_start: 0.8847 (mmm) cc_final: 0.8585 (mmm) REVERT: D 276 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7390 (pt0) REVERT: D 296 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7911 (mm-30) REVERT: D 305 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8188 (tttp) REVERT: D 362 MET cc_start: 0.7818 (ttt) cc_final: 0.7521 (ttt) REVERT: E 214 LEU cc_start: 0.7896 (mt) cc_final: 0.7687 (mt) REVERT: E 296 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7835 (tp30) REVERT: E 420 ARG cc_start: 0.8820 (mtp180) cc_final: 0.8292 (tpp-160) REVERT: E 462 TYR cc_start: 0.6102 (m-80) cc_final: 0.5861 (m-10) REVERT: F 11 ILE cc_start: 0.9023 (mm) cc_final: 0.8716 (mp) REVERT: F 88 MET cc_start: 0.7691 (ptm) cc_final: 0.7145 (ptm) REVERT: F 89 LEU cc_start: 0.8261 (mt) cc_final: 0.7930 (tp) REVERT: F 194 MET cc_start: 0.8347 (mtm) cc_final: 0.7894 (mmm) REVERT: F 237 MET cc_start: 0.6752 (mpp) cc_final: 0.6543 (mpp) REVERT: G 144 GLU cc_start: 0.8366 (tt0) cc_final: 0.7843 (tm-30) REVERT: H 39 ARG cc_start: 0.6877 (ttp80) cc_final: 0.6246 (tmt-80) REVERT: J 78 GLU cc_start: 0.7705 (tp30) cc_final: 0.7434 (mt-10) REVERT: J 91 LEU cc_start: 0.7249 (mt) cc_final: 0.7001 (mt) REVERT: J 99 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6658 (pm20) REVERT: J 126 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7348 (mp0) REVERT: L 84 ARG cc_start: 0.6420 (ttt180) cc_final: 0.5442 (ttp80) outliers start: 2 outliers final: 2 residues processed: 297 average time/residue: 0.4293 time to fit residues: 201.9673 Evaluate side-chains 217 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 215 time to evaluate : 3.625 ------------------------------------------------------------------------------- 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: 4.9990 chunk 255 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 340 optimal weight: 9.9990 chunk 360 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 322 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** 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** F 413 GLN G 68 GLN ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 30015 Z= 0.335 Angle : 0.646 12.474 40658 Z= 0.330 Chirality : 0.047 0.198 4560 Planarity : 0.005 0.056 5330 Dihedral : 4.797 20.241 4180 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.62 % 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: -0.28 (0.14), residues: 3764 helix: 0.84 (0.13), residues: 1559 sheet: -0.56 (0.22), residues: 571 loop : -1.00 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 100 HIS 0.008 0.002 HIS D 375 PHE 0.028 0.002 PHE A 269 TYR 0.019 0.002 TYR F 463 ARG 0.006 0.001 ARG D 360 *********************** 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 304 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 303 time to evaluate : 3.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.7882 (mtp) cc_final: 0.7073 (mmm) REVERT: A 175 LEU cc_start: 0.8393 (mt) cc_final: 0.7664 (tp) REVERT: A 179 THR cc_start: 0.8386 (m) cc_final: 0.8083 (p) REVERT: A 220 MET cc_start: 0.7815 (tpp) cc_final: 0.7342 (ttp) REVERT: A 282 MET cc_start: 0.8240 (mmm) cc_final: 0.7941 (mmm) REVERT: A 498 ASN cc_start: 0.8388 (t0) cc_final: 0.8141 (t0) REVERT: A 550 ARG cc_start: 0.7355 (tpp-160) cc_final: 0.6639 (ttt90) REVERT: B 93 ARG cc_start: 0.7370 (mtm-85) cc_final: 0.6920 (mtm-85) REVERT: B 133 MET cc_start: 0.8052 (mtp) cc_final: 0.7377 (tmm) REVERT: B 265 VAL cc_start: 0.8084 (t) cc_final: 0.7756 (t) REVERT: B 282 MET cc_start: 0.8814 (tpt) cc_final: 0.8205 (mpp) REVERT: B 391 MET cc_start: 0.6862 (mmt) cc_final: 0.5648 (mmm) REVERT: C 114 GLU cc_start: 0.8237 (mp0) cc_final: 0.7469 (pm20) REVERT: C 161 LYS cc_start: 0.7730 (mmtm) cc_final: 0.7335 (mmtt) REVERT: C 183 MET cc_start: 0.8777 (mtt) cc_final: 0.8187 (mtp) REVERT: C 282 MET cc_start: 0.7971 (tpt) cc_final: 0.7477 (tpt) REVERT: C 294 MET cc_start: 0.8684 (mtt) cc_final: 0.8359 (mtt) REVERT: C 520 LEU cc_start: 0.8160 (mt) cc_final: 0.7765 (tt) REVERT: C 556 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7945 (tp30) REVERT: D 142 ASN cc_start: 0.8318 (m110) cc_final: 0.7527 (m110) REVERT: D 190 VAL cc_start: 0.7867 (t) cc_final: 0.7576 (p) REVERT: D 230 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7973 (mt-10) REVERT: D 259 ASP cc_start: 0.7473 (t0) cc_final: 0.7198 (t0) REVERT: D 260 MET cc_start: 0.8955 (mmm) cc_final: 0.8633 (mmt) REVERT: D 276 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7140 (pt0) REVERT: D 296 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7822 (mm-30) REVERT: D 305 LYS cc_start: 0.8577 (mtmt) cc_final: 0.8141 (tttp) REVERT: E 214 LEU cc_start: 0.7983 (mt) cc_final: 0.7740 (mt) REVERT: E 296 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7866 (tp30) REVERT: E 420 ARG cc_start: 0.8775 (mtp180) cc_final: 0.8246 (tpp-160) REVERT: F 11 ILE cc_start: 0.9009 (mm) cc_final: 0.8681 (mp) REVERT: F 88 MET cc_start: 0.7638 (ptm) cc_final: 0.7034 (ptm) REVERT: F 89 LEU cc_start: 0.8090 (mt) cc_final: 0.7829 (tp) REVERT: F 194 MET cc_start: 0.8444 (mtm) cc_final: 0.8024 (mmm) REVERT: F 287 MET cc_start: 0.7163 (ttm) cc_final: 0.6840 (ttm) REVERT: G 144 GLU cc_start: 0.8347 (tt0) cc_final: 0.7771 (tm-30) REVERT: H 39 ARG cc_start: 0.7033 (ttp80) cc_final: 0.6366 (tmt-80) REVERT: J 78 GLU cc_start: 0.7588 (tp30) cc_final: 0.7287 (mt-10) REVERT: J 99 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6836 (pm20) REVERT: J 126 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7369 (mp0) REVERT: J 130 HIS cc_start: 0.6000 (m170) cc_final: 0.5539 (m170) REVERT: J 165 ASN cc_start: 0.6552 (p0) cc_final: 0.6134 (p0) REVERT: L 84 ARG cc_start: 0.6307 (ttt90) cc_final: 0.5563 (ttp80) REVERT: L 88 ARG cc_start: 0.7449 (ttp80) cc_final: 0.7211 (ttp80) outliers start: 1 outliers final: 1 residues processed: 304 average time/residue: 0.4115 time to fit residues: 200.1373 Evaluate side-chains 217 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 3.676 ------------------------------------------------------------------------------- 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: 9.9990 chunk 5 optimal weight: 7.9990 chunk 268 optimal weight: 5.9990 chunk 148 optimal weight: 0.0870 chunk 307 optimal weight: 2.9990 chunk 249 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 323 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN C 316 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN L 165 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 30015 Z= 0.306 Angle : 0.618 11.862 40658 Z= 0.315 Chirality : 0.046 0.171 4560 Planarity : 0.005 0.053 5330 Dihedral : 4.716 19.154 4180 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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: -0.28 (0.14), residues: 3764 helix: 0.89 (0.13), residues: 1561 sheet: -0.60 (0.22), residues: 557 loop : -1.04 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J 100 HIS 0.006 0.001 HIS L 130 PHE 0.021 0.002 PHE G 40 TYR 0.028 0.002 TYR E 349 ARG 0.006 0.000 ARG K 87 *********************** 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 290 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 4.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.7536 (mmm) cc_final: 0.7080 (mtp) REVERT: A 133 MET cc_start: 0.7833 (mtp) cc_final: 0.7014 (mmm) REVERT: A 175 LEU cc_start: 0.8225 (mt) cc_final: 0.7729 (tp) REVERT: A 220 MET cc_start: 0.7808 (tpp) cc_final: 0.7352 (ttp) REVERT: A 498 ASN cc_start: 0.8372 (t0) cc_final: 0.8152 (t0) REVERT: A 550 ARG cc_start: 0.7323 (tpp-160) cc_final: 0.6722 (ttt90) REVERT: B 93 ARG cc_start: 0.7358 (mtm-85) cc_final: 0.6861 (mtm-85) REVERT: B 133 MET cc_start: 0.8087 (mtp) cc_final: 0.7374 (tmm) REVERT: C 161 LYS cc_start: 0.7715 (mmtm) cc_final: 0.7294 (mmtt) REVERT: C 183 MET cc_start: 0.8797 (mtt) cc_final: 0.8156 (mtp) REVERT: C 239 GLN cc_start: 0.8099 (mt0) cc_final: 0.7787 (mp10) REVERT: C 282 MET cc_start: 0.7999 (tpt) cc_final: 0.7493 (tpt) REVERT: C 520 LEU cc_start: 0.8253 (mt) cc_final: 0.7820 (tt) REVERT: C 556 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8003 (tp30) REVERT: D 142 ASN cc_start: 0.7699 (m110) cc_final: 0.7304 (m110) REVERT: D 230 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7965 (mt-10) REVERT: D 260 MET cc_start: 0.8993 (mmm) cc_final: 0.8666 (mmt) REVERT: D 276 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7063 (pt0) REVERT: D 296 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7808 (mm-30) REVERT: D 305 LYS cc_start: 0.8616 (mtmt) cc_final: 0.8154 (tttp) REVERT: E 214 LEU cc_start: 0.7952 (mt) cc_final: 0.7551 (mt) REVERT: E 296 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7730 (tp30) REVERT: E 410 ARG cc_start: 0.7479 (mmt180) cc_final: 0.7003 (ttm170) REVERT: E 420 ARG cc_start: 0.8746 (mtp180) cc_final: 0.8193 (tpp-160) REVERT: F 11 ILE cc_start: 0.8991 (mm) cc_final: 0.8684 (mp) REVERT: F 88 MET cc_start: 0.7544 (ptm) cc_final: 0.6982 (ptm) REVERT: F 89 LEU cc_start: 0.8063 (mt) cc_final: 0.7709 (tp) REVERT: F 194 MET cc_start: 0.8426 (mtm) cc_final: 0.8010 (mmm) REVERT: F 316 MET cc_start: 0.8561 (mtm) cc_final: 0.8172 (mtp) REVERT: G 144 GLU cc_start: 0.8330 (tt0) cc_final: 0.7773 (tm-30) REVERT: H 39 ARG cc_start: 0.6994 (ttp80) cc_final: 0.6346 (tmt-80) REVERT: J 78 GLU cc_start: 0.7578 (tp30) cc_final: 0.7251 (mt-10) REVERT: J 126 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7433 (mp0) REVERT: J 165 ASN cc_start: 0.5742 (p0) cc_final: 0.5498 (p0) REVERT: L 84 ARG cc_start: 0.6271 (ttt90) cc_final: 0.5573 (ttp80) REVERT: L 127 ASP cc_start: 0.7024 (m-30) cc_final: 0.6636 (m-30) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.4570 time to fit residues: 211.5160 Evaluate side-chains 211 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 3.564 ------------------------------------------------------------------------------- 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: 7.9990 chunk 324 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 360 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 30015 Z= 0.305 Angle : 0.622 11.553 40658 Z= 0.316 Chirality : 0.046 0.173 4560 Planarity : 0.005 0.077 5330 Dihedral : 4.698 20.117 4180 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: -0.26 (0.14), residues: 3764 helix: 0.93 (0.13), residues: 1554 sheet: -0.48 (0.23), residues: 531 loop : -1.09 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP J 100 HIS 0.005 0.001 HIS F 249 PHE 0.031 0.002 PHE A 269 TYR 0.021 0.002 TYR E 349 ARG 0.007 0.000 ARG L 88 *********************** 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 278 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 3.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.7674 (mmm) cc_final: 0.7235 (mtp) REVERT: A 133 MET cc_start: 0.7894 (mtp) cc_final: 0.7026 (mmm) REVERT: A 175 LEU cc_start: 0.8213 (mt) cc_final: 0.7720 (tp) REVERT: A 220 MET cc_start: 0.7810 (tpp) cc_final: 0.7334 (ttp) REVERT: A 282 MET cc_start: 0.8463 (mmp) cc_final: 0.8170 (mmm) REVERT: A 336 GLU cc_start: 0.8288 (tp30) cc_final: 0.7820 (tp30) REVERT: A 498 ASN cc_start: 0.8396 (t0) cc_final: 0.8195 (t0) REVERT: A 550 ARG cc_start: 0.7380 (tpp-160) cc_final: 0.6742 (ttt90) REVERT: B 1 MET cc_start: 0.7932 (mmp) cc_final: 0.7702 (mmt) REVERT: B 93 ARG cc_start: 0.7385 (mtm-85) cc_final: 0.6881 (mtm-85) REVERT: B 133 MET cc_start: 0.8049 (mtp) cc_final: 0.7376 (tmm) REVERT: B 175 LEU cc_start: 0.8408 (mt) cc_final: 0.8185 (mt) REVERT: B 391 MET cc_start: 0.6149 (mmt) cc_final: 0.5927 (mmm) REVERT: C 114 GLU cc_start: 0.7957 (mp0) cc_final: 0.7524 (pm20) REVERT: C 161 LYS cc_start: 0.7703 (mmtm) cc_final: 0.7390 (mmtt) REVERT: C 183 MET cc_start: 0.8788 (mtt) cc_final: 0.8161 (mtp) REVERT: C 239 GLN cc_start: 0.8114 (mt0) cc_final: 0.7805 (mp10) REVERT: C 282 MET cc_start: 0.7918 (tpt) cc_final: 0.7431 (tpt) REVERT: C 509 MET cc_start: 0.8717 (mmp) cc_final: 0.8454 (mmt) REVERT: C 520 LEU cc_start: 0.8283 (mt) cc_final: 0.7851 (tt) REVERT: C 556 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8043 (tp30) REVERT: D 141 MET cc_start: 0.8168 (mtp) cc_final: 0.7933 (mtp) REVERT: D 142 ASN cc_start: 0.7954 (m110) cc_final: 0.7166 (p0) REVERT: D 237 MET cc_start: 0.8618 (mmm) cc_final: 0.8277 (mmm) REVERT: D 260 MET cc_start: 0.8983 (mmm) cc_final: 0.8690 (mmt) REVERT: D 276 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7663 (pt0) REVERT: D 296 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7774 (mm-30) REVERT: D 305 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8171 (tttp) REVERT: E 214 LEU cc_start: 0.8038 (mt) cc_final: 0.7769 (mt) REVERT: E 296 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7746 (tp30) REVERT: E 410 ARG cc_start: 0.7525 (mmt180) cc_final: 0.7070 (ttm170) REVERT: E 420 ARG cc_start: 0.8725 (mtp180) cc_final: 0.8169 (tpp-160) REVERT: F 11 ILE cc_start: 0.8993 (mm) cc_final: 0.8705 (mp) REVERT: F 88 MET cc_start: 0.7455 (ptm) cc_final: 0.6889 (ptm) REVERT: F 89 LEU cc_start: 0.8101 (mt) cc_final: 0.7744 (tp) REVERT: F 194 MET cc_start: 0.8474 (mtm) cc_final: 0.8029 (mmm) REVERT: G 144 GLU cc_start: 0.8331 (tt0) cc_final: 0.7784 (tm-30) REVERT: G 185 GLN cc_start: 0.7852 (tp40) cc_final: 0.7622 (tp40) REVERT: H 39 ARG cc_start: 0.6991 (ttp80) cc_final: 0.6426 (tmt170) REVERT: J 78 GLU cc_start: 0.7574 (tp30) cc_final: 0.7240 (mt-10) REVERT: J 126 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7518 (mp0) REVERT: J 165 ASN cc_start: 0.5675 (p0) cc_final: 0.5433 (p0) REVERT: K 104 MET cc_start: 0.4109 (mpp) cc_final: 0.3889 (mpp) REVERT: L 84 ARG cc_start: 0.6279 (ttt90) cc_final: 0.5581 (ttp80) REVERT: L 127 ASP cc_start: 0.7015 (m-30) cc_final: 0.6732 (m-30) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.4317 time to fit residues: 190.1363 Evaluate side-chains 202 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 4.474 ------------------------------------------------------------------------------- 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: 10.0000 chunk 40 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 263 optimal weight: 20.0000 chunk 204 optimal weight: 0.9980 chunk 303 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 359 optimal weight: 4.9990 chunk 224 optimal weight: 9.9990 chunk 219 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN C 316 GLN ** 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** E 249 HIS ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 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 : 0.004 0.042 30015 Z= 0.260 Angle : 0.595 10.894 40658 Z= 0.301 Chirality : 0.045 0.250 4560 Planarity : 0.005 0.062 5330 Dihedral : 4.579 19.906 4180 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 0.97 (0.13), residues: 1568 sheet: -0.40 (0.23), residues: 543 loop : -1.05 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP J 100 HIS 0.005 0.001 HIS J 130 PHE 0.026 0.002 PHE G 40 TYR 0.016 0.001 TYR E 349 ARG 0.008 0.000 ARG L 88 *********************** 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 287 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.7669 (mmm) cc_final: 0.7328 (mtp) REVERT: A 24 MET cc_start: 0.8176 (tpp) cc_final: 0.7888 (tpp) REVERT: A 133 MET cc_start: 0.7795 (mtp) cc_final: 0.6955 (mmm) REVERT: A 175 LEU cc_start: 0.8192 (mt) cc_final: 0.7708 (tp) REVERT: A 220 MET cc_start: 0.7896 (tpp) cc_final: 0.7387 (ttp) REVERT: A 282 MET cc_start: 0.8492 (mmp) cc_final: 0.8229 (mpp) REVERT: A 336 GLU cc_start: 0.8304 (tp30) cc_final: 0.7838 (tp30) REVERT: A 550 ARG cc_start: 0.7419 (tpp-160) cc_final: 0.6762 (ttt90) REVERT: B 93 ARG cc_start: 0.7358 (mtm-85) cc_final: 0.6880 (mtm-85) REVERT: B 133 MET cc_start: 0.8082 (mtp) cc_final: 0.7358 (tmm) REVERT: B 282 MET cc_start: 0.8600 (mmm) cc_final: 0.8383 (mmm) REVERT: C 161 LYS cc_start: 0.7668 (mmtm) cc_final: 0.7354 (mmtt) REVERT: C 183 MET cc_start: 0.8790 (mtt) cc_final: 0.8153 (mtp) REVERT: C 239 GLN cc_start: 0.8122 (mt0) cc_final: 0.7880 (mp10) REVERT: C 240 SER cc_start: 0.9569 (m) cc_final: 0.9321 (p) REVERT: C 282 MET cc_start: 0.7902 (tpt) cc_final: 0.7411 (tpt) REVERT: C 509 MET cc_start: 0.8717 (mmp) cc_final: 0.8458 (mmt) REVERT: C 520 LEU cc_start: 0.8294 (mt) cc_final: 0.7844 (tt) REVERT: C 556 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8087 (tp30) REVERT: D 52 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7540 (tp30) REVERT: D 142 ASN cc_start: 0.7683 (m110) cc_final: 0.7046 (p0) REVERT: D 276 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7580 (pt0) REVERT: D 296 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7758 (mm-30) REVERT: D 305 LYS cc_start: 0.8554 (mtmt) cc_final: 0.8173 (tttp) REVERT: E 214 LEU cc_start: 0.8013 (mt) cc_final: 0.7750 (mt) REVERT: E 296 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7835 (tp30) REVERT: E 410 ARG cc_start: 0.7512 (mmt180) cc_final: 0.7048 (ttm170) REVERT: E 420 ARG cc_start: 0.8670 (mtp180) cc_final: 0.8101 (tpp-160) REVERT: F 11 ILE cc_start: 0.8974 (mm) cc_final: 0.8681 (mp) REVERT: F 88 MET cc_start: 0.7345 (ptm) cc_final: 0.6809 (ptm) REVERT: F 89 LEU cc_start: 0.8109 (mt) cc_final: 0.7778 (tp) REVERT: F 194 MET cc_start: 0.8377 (mtm) cc_final: 0.8033 (mmm) REVERT: F 316 MET cc_start: 0.8567 (mtm) cc_final: 0.8192 (mtp) REVERT: F 327 ASP cc_start: 0.8080 (t70) cc_final: 0.7734 (t0) REVERT: G 68 GLN cc_start: 0.5298 (tt0) cc_final: 0.5067 (pp30) REVERT: G 144 GLU cc_start: 0.8285 (tt0) cc_final: 0.7708 (tm-30) REVERT: G 185 GLN cc_start: 0.7795 (tp40) cc_final: 0.7585 (tp40) REVERT: H 39 ARG cc_start: 0.6967 (ttp80) cc_final: 0.6318 (tmt-80) REVERT: J 78 GLU cc_start: 0.7594 (tp30) cc_final: 0.7256 (mt-10) REVERT: J 126 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7411 (mp0) REVERT: J 165 ASN cc_start: 0.5614 (p0) cc_final: 0.5399 (p0) REVERT: L 84 ARG cc_start: 0.6320 (ttt90) cc_final: 0.5607 (ttp80) REVERT: L 127 ASP cc_start: 0.7034 (m-30) cc_final: 0.6753 (m-30) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.4126 time to fit residues: 186.5531 Evaluate side-chains 208 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 3.189 ------------------------------------------------------------------------------- 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: 20.0000 chunk 143 optimal weight: 6.9990 chunk 214 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 282 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 290 ASN ** 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** ** 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: 0.7485 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30015 Z= 0.314 Angle : 0.633 11.439 40658 Z= 0.321 Chirality : 0.046 0.230 4560 Planarity : 0.005 0.074 5330 Dihedral : 4.679 21.810 4180 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: -0.25 (0.14), residues: 3764 helix: 0.94 (0.13), residues: 1563 sheet: -0.46 (0.23), residues: 541 loop : -1.11 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP J 100 HIS 0.005 0.001 HIS F 249 PHE 0.024 0.002 PHE A 269 TYR 0.022 0.002 TYR A 500 ARG 0.005 0.000 ARG G 193 *********************** 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 268 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.7642 (mmm) cc_final: 0.7344 (mtp) REVERT: A 133 MET cc_start: 0.7863 (mtp) cc_final: 0.7063 (mmm) REVERT: A 175 LEU cc_start: 0.8204 (mt) cc_final: 0.7735 (tp) REVERT: A 220 MET cc_start: 0.7889 (tpp) cc_final: 0.7390 (ttp) REVERT: A 282 MET cc_start: 0.8570 (mmp) cc_final: 0.8283 (mpp) REVERT: A 336 GLU cc_start: 0.8292 (tp30) cc_final: 0.7842 (tp30) REVERT: A 550 ARG cc_start: 0.7435 (tpp-160) cc_final: 0.6826 (ttt90) REVERT: B 93 ARG cc_start: 0.7371 (mtm-85) cc_final: 0.6864 (mtm-85) REVERT: B 133 MET cc_start: 0.8060 (mtp) cc_final: 0.7396 (tmm) REVERT: B 262 MET cc_start: 0.8834 (pmm) cc_final: 0.8187 (pmm) REVERT: C 38 GLU cc_start: 0.8067 (tt0) cc_final: 0.7785 (tt0) REVERT: C 161 LYS cc_start: 0.7611 (mmtm) cc_final: 0.7316 (mmtt) REVERT: C 183 MET cc_start: 0.8749 (mtt) cc_final: 0.8147 (mtp) REVERT: C 239 GLN cc_start: 0.8168 (mt0) cc_final: 0.7917 (mp10) REVERT: C 240 SER cc_start: 0.9574 (m) cc_final: 0.9331 (p) REVERT: C 282 MET cc_start: 0.7948 (tpt) cc_final: 0.7460 (tpt) REVERT: C 509 MET cc_start: 0.8695 (mmp) cc_final: 0.8480 (mmt) REVERT: C 520 LEU cc_start: 0.8338 (mt) cc_final: 0.7875 (tt) REVERT: C 556 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8135 (tp30) REVERT: D 52 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7654 (tp30) REVERT: D 141 MET cc_start: 0.8037 (mtp) cc_final: 0.7835 (mtp) REVERT: D 142 ASN cc_start: 0.7721 (m110) cc_final: 0.7112 (p0) REVERT: D 276 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7475 (pt0) REVERT: D 296 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7769 (mm-30) REVERT: D 305 LYS cc_start: 0.8572 (mtmt) cc_final: 0.8181 (tttp) REVERT: E 214 LEU cc_start: 0.8035 (mt) cc_final: 0.7765 (mt) REVERT: E 410 ARG cc_start: 0.7533 (mmt180) cc_final: 0.7081 (ttm170) REVERT: E 420 ARG cc_start: 0.8681 (mtp180) cc_final: 0.7940 (tpp-160) REVERT: F 11 ILE cc_start: 0.9002 (mm) cc_final: 0.8726 (mp) REVERT: F 88 MET cc_start: 0.7364 (ptm) cc_final: 0.6811 (ptm) REVERT: F 89 LEU cc_start: 0.8121 (mt) cc_final: 0.7774 (tp) REVERT: F 194 MET cc_start: 0.8387 (mtm) cc_final: 0.8051 (mmm) REVERT: F 316 MET cc_start: 0.8593 (mtm) cc_final: 0.8199 (mtp) REVERT: F 327 ASP cc_start: 0.8218 (t70) cc_final: 0.7879 (t0) REVERT: G 68 GLN cc_start: 0.5262 (tt0) cc_final: 0.5060 (pp30) REVERT: G 144 GLU cc_start: 0.8311 (tt0) cc_final: 0.7690 (tm-30) REVERT: G 185 GLN cc_start: 0.7856 (tp40) cc_final: 0.7624 (tp40) REVERT: H 39 ARG cc_start: 0.6959 (ttp80) cc_final: 0.6321 (tmt-80) REVERT: J 78 GLU cc_start: 0.7571 (tp30) cc_final: 0.7250 (mt-10) REVERT: J 126 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7359 (mp0) REVERT: J 165 ASN cc_start: 0.5677 (p0) cc_final: 0.5401 (p0) REVERT: L 74 GLN cc_start: 0.6777 (pt0) cc_final: 0.6118 (tp-100) REVERT: L 84 ARG cc_start: 0.6345 (ttt90) cc_final: 0.5654 (ttp80) REVERT: L 127 ASP cc_start: 0.7024 (m-30) cc_final: 0.6764 (m-30) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.4133 time to fit residues: 177.8043 Evaluate side-chains 207 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 3.663 ------------------------------------------------------------------------------- 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: 0.8980 chunk 344 optimal weight: 4.9990 chunk 314 optimal weight: 10.0000 chunk 335 optimal weight: 30.0000 chunk 201 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 302 optimal weight: 8.9990 chunk 316 optimal weight: 20.0000 chunk 333 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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** ** 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** ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30015 Z= 0.241 Angle : 0.595 11.858 40658 Z= 0.300 Chirality : 0.045 0.218 4560 Planarity : 0.005 0.066 5330 Dihedral : 4.532 21.684 4180 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 1.05 (0.14), residues: 1566 sheet: -0.55 (0.22), residues: 555 loop : -1.04 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP J 100 HIS 0.004 0.001 HIS E 458 PHE 0.019 0.001 PHE A 269 TYR 0.016 0.001 TYR D 331 ARG 0.009 0.000 ARG L 88 *********************** 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 278 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.7634 (mmm) cc_final: 0.7184 (mtp) REVERT: A 133 MET cc_start: 0.7837 (mtp) cc_final: 0.7059 (mmm) REVERT: A 175 LEU cc_start: 0.8212 (mt) cc_final: 0.7743 (tp) REVERT: A 220 MET cc_start: 0.7882 (tpp) cc_final: 0.7472 (ttp) REVERT: A 282 MET cc_start: 0.8549 (mmp) cc_final: 0.8270 (tpp) REVERT: A 311 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6754 (tt0) REVERT: A 336 GLU cc_start: 0.8298 (tp30) cc_final: 0.7855 (tp30) REVERT: A 550 ARG cc_start: 0.7496 (tpp-160) cc_final: 0.6833 (ttt90) REVERT: B 93 ARG cc_start: 0.7360 (mtm-85) cc_final: 0.6871 (mtm-85) REVERT: B 133 MET cc_start: 0.8073 (mtp) cc_final: 0.7389 (tmm) REVERT: B 262 MET cc_start: 0.8797 (pmm) cc_final: 0.8217 (pmm) REVERT: B 282 MET cc_start: 0.8656 (mmm) cc_final: 0.8411 (mmm) REVERT: B 294 MET cc_start: 0.7999 (mtp) cc_final: 0.7661 (mtp) REVERT: B 531 LYS cc_start: 0.7580 (pttm) cc_final: 0.7290 (ttmm) REVERT: C 38 GLU cc_start: 0.8049 (tt0) cc_final: 0.7782 (tt0) REVERT: C 161 LYS cc_start: 0.7620 (mmtm) cc_final: 0.7269 (mmtt) REVERT: C 183 MET cc_start: 0.8798 (mtt) cc_final: 0.8172 (mtp) REVERT: C 239 GLN cc_start: 0.8163 (mt0) cc_final: 0.7903 (mp10) REVERT: C 240 SER cc_start: 0.9569 (m) cc_final: 0.9337 (p) REVERT: C 282 MET cc_start: 0.7938 (tpt) cc_final: 0.7442 (tpt) REVERT: C 509 MET cc_start: 0.8710 (mmp) cc_final: 0.8488 (mmt) REVERT: C 556 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8138 (tp30) REVERT: D 52 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7606 (tp30) REVERT: D 141 MET cc_start: 0.8142 (mtp) cc_final: 0.7913 (mtp) REVERT: D 142 ASN cc_start: 0.7891 (m110) cc_final: 0.7319 (p0) REVERT: D 276 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7395 (pt0) REVERT: D 296 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7560 (mm-30) REVERT: D 305 LYS cc_start: 0.8565 (mtmt) cc_final: 0.8167 (tttp) REVERT: E 214 LEU cc_start: 0.8047 (mt) cc_final: 0.7762 (mt) REVERT: E 237 MET cc_start: 0.7989 (mmm) cc_final: 0.7529 (mmt) REVERT: E 410 ARG cc_start: 0.7528 (mmt180) cc_final: 0.7078 (ttm170) REVERT: E 420 ARG cc_start: 0.8473 (mtp180) cc_final: 0.7976 (tpp-160) REVERT: F 11 ILE cc_start: 0.8962 (mm) cc_final: 0.8684 (mp) REVERT: F 78 ASP cc_start: 0.6614 (t70) cc_final: 0.6165 (t0) REVERT: F 88 MET cc_start: 0.7354 (ptm) cc_final: 0.6813 (ptm) REVERT: F 89 LEU cc_start: 0.8136 (mt) cc_final: 0.7793 (tp) REVERT: F 141 MET cc_start: 0.8372 (mtp) cc_final: 0.8115 (mtp) REVERT: F 194 MET cc_start: 0.8395 (mtm) cc_final: 0.8062 (mmm) REVERT: F 237 MET cc_start: 0.6310 (mpp) cc_final: 0.6108 (mpp) REVERT: F 287 MET cc_start: 0.6141 (ttm) cc_final: 0.5701 (ttm) REVERT: F 316 MET cc_start: 0.8591 (mtm) cc_final: 0.8183 (mtp) REVERT: F 327 ASP cc_start: 0.8199 (t70) cc_final: 0.7908 (t0) REVERT: G 68 GLN cc_start: 0.5251 (tt0) cc_final: 0.5029 (pp30) REVERT: G 144 GLU cc_start: 0.8322 (tt0) cc_final: 0.7707 (tm-30) REVERT: G 185 GLN cc_start: 0.7881 (tp40) cc_final: 0.7647 (tp40) REVERT: H 39 ARG cc_start: 0.6908 (ttp80) cc_final: 0.6278 (tmt-80) REVERT: J 78 GLU cc_start: 0.7565 (tp30) cc_final: 0.7209 (mt-10) REVERT: J 126 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7370 (mp0) REVERT: L 74 GLN cc_start: 0.6795 (pt0) cc_final: 0.6168 (tp-100) REVERT: L 84 ARG cc_start: 0.6365 (ttt90) cc_final: 0.5684 (ttp80) REVERT: L 88 ARG cc_start: 0.7740 (ttp80) cc_final: 0.7405 (ttp80) REVERT: L 127 ASP cc_start: 0.7032 (m-30) cc_final: 0.6770 (m-30) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.4149 time to fit residues: 182.9166 Evaluate side-chains 210 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 3.468 ------------------------------------------------------------------------------- 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: 0.0470 chunk 354 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 246 optimal weight: 0.9980 chunk 371 optimal weight: 0.3980 chunk 342 optimal weight: 9.9990 chunk 295 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- 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 81 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 F 142 ASN ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 30015 Z= 0.154 Angle : 0.565 11.561 40658 Z= 0.281 Chirality : 0.044 0.212 4560 Planarity : 0.004 0.059 5330 Dihedral : 4.224 25.859 4180 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 0.09 (0.14), residues: 3764 helix: 1.27 (0.14), residues: 1569 sheet: -0.45 (0.22), residues: 567 loop : -0.91 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP J 100 HIS 0.004 0.001 HIS J 130 PHE 0.015 0.001 PHE B 559 TYR 0.020 0.001 TYR E 462 ARG 0.007 0.000 ARG L 88 ********************** 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 299 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.7618 (mmm) cc_final: 0.7176 (mtp) REVERT: A 24 MET cc_start: 0.7801 (tpp) cc_final: 0.7580 (tpp) REVERT: A 133 MET cc_start: 0.7750 (mtp) cc_final: 0.6981 (mmm) REVERT: A 175 LEU cc_start: 0.8233 (mt) cc_final: 0.7753 (tp) REVERT: A 220 MET cc_start: 0.7864 (tpp) cc_final: 0.7343 (ttp) REVERT: A 282 MET cc_start: 0.8538 (mmp) cc_final: 0.8233 (mpp) REVERT: A 311 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6790 (tt0) REVERT: A 330 TRP cc_start: 0.8008 (t60) cc_final: 0.7725 (t-100) REVERT: A 336 GLU cc_start: 0.8266 (tp30) cc_final: 0.7853 (tp30) REVERT: A 550 ARG cc_start: 0.7403 (tpp-160) cc_final: 0.6812 (ttt-90) REVERT: B 93 ARG cc_start: 0.7414 (mtm-85) cc_final: 0.6880 (mtm-85) REVERT: B 133 MET cc_start: 0.8089 (mtp) cc_final: 0.7366 (tmm) REVERT: B 262 MET cc_start: 0.8769 (pmm) cc_final: 0.8287 (pmm) REVERT: B 294 MET cc_start: 0.7905 (mtp) cc_final: 0.7361 (mtp) REVERT: B 531 LYS cc_start: 0.7509 (pttm) cc_final: 0.7264 (ttmm) REVERT: C 38 GLU cc_start: 0.8061 (tt0) cc_final: 0.7724 (tt0) REVERT: C 161 LYS cc_start: 0.7535 (mmtm) cc_final: 0.7205 (mmtt) REVERT: C 183 MET cc_start: 0.8910 (mtt) cc_final: 0.8309 (mtp) REVERT: C 239 GLN cc_start: 0.8145 (mt0) cc_final: 0.7857 (mp10) REVERT: C 240 SER cc_start: 0.9542 (m) cc_final: 0.9310 (p) REVERT: C 282 MET cc_start: 0.7937 (tpt) cc_final: 0.7456 (tpt) REVERT: C 509 MET cc_start: 0.8712 (mmp) cc_final: 0.8463 (mmt) REVERT: C 556 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8042 (tp30) REVERT: D 142 ASN cc_start: 0.7605 (m110) cc_final: 0.7002 (p0) REVERT: D 275 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8001 (pm20) REVERT: D 276 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7532 (pt0) REVERT: D 296 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7533 (mm-30) REVERT: D 305 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8147 (tttp) REVERT: D 407 ASN cc_start: 0.7664 (m-40) cc_final: 0.7457 (m110) REVERT: E 214 LEU cc_start: 0.7980 (mt) cc_final: 0.7754 (mt) REVERT: E 410 ARG cc_start: 0.7494 (mmt180) cc_final: 0.6977 (ttm110) REVERT: E 420 ARG cc_start: 0.8368 (mtp180) cc_final: 0.7916 (tpp-160) REVERT: F 11 ILE cc_start: 0.8876 (mm) cc_final: 0.8670 (mp) REVERT: F 78 ASP cc_start: 0.6568 (t70) cc_final: 0.6138 (t0) REVERT: F 88 MET cc_start: 0.7362 (ptm) cc_final: 0.6850 (ptm) REVERT: F 89 LEU cc_start: 0.8131 (mt) cc_final: 0.7812 (tp) REVERT: F 141 MET cc_start: 0.8297 (mtp) cc_final: 0.8040 (mtp) REVERT: F 287 MET cc_start: 0.6130 (ttm) cc_final: 0.5874 (ttm) REVERT: F 316 MET cc_start: 0.8551 (mtm) cc_final: 0.8117 (mtp) REVERT: F 327 ASP cc_start: 0.8165 (t70) cc_final: 0.7890 (t0) REVERT: G 68 GLN cc_start: 0.5149 (tt0) cc_final: 0.4928 (pp30) REVERT: G 144 GLU cc_start: 0.8356 (tt0) cc_final: 0.7786 (tm-30) REVERT: G 185 GLN cc_start: 0.7863 (tp40) cc_final: 0.7567 (tp40) REVERT: H 39 ARG cc_start: 0.6959 (ttp80) cc_final: 0.6309 (tmt-80) REVERT: J 78 GLU cc_start: 0.7564 (tp30) cc_final: 0.7241 (mt-10) REVERT: L 74 GLN cc_start: 0.6826 (pt0) cc_final: 0.6198 (tp-100) REVERT: L 84 ARG cc_start: 0.6339 (ttt90) cc_final: 0.5604 (ttp80) REVERT: L 88 ARG cc_start: 0.7763 (ttp80) cc_final: 0.7464 (ttp80) REVERT: L 110 GLU cc_start: 0.6256 (pt0) cc_final: 0.5185 (tp30) REVERT: L 127 ASP cc_start: 0.7093 (m-30) cc_final: 0.6698 (m-30) REVERT: L 172 ASP cc_start: 0.7605 (m-30) cc_final: 0.7220 (m-30) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.4620 time to fit residues: 222.4652 Evaluate side-chains 215 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.762 ------------------------------------------------------------------------------- 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: 0.0770 chunk 315 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 272 optimal weight: 0.0770 chunk 43 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 296 optimal weight: 0.7980 chunk 124 optimal weight: 0.4980 chunk 304 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS A 477 GLN C 316 GLN D 23 ASN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.064744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.053302 restraints weight = 117546.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.054680 restraints weight = 76320.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.055073 restraints weight = 52022.462| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30015 Z= 0.142 Angle : 0.554 10.901 40658 Z= 0.275 Chirality : 0.043 0.210 4560 Planarity : 0.004 0.051 5330 Dihedral : 4.020 21.613 4180 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.28 (0.14), residues: 3764 helix: 1.42 (0.14), residues: 1573 sheet: -0.36 (0.22), residues: 584 loop : -0.81 (0.16), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 100 HIS 0.010 0.001 HIS A 283 PHE 0.030 0.001 PHE G 108 TYR 0.015 0.001 TYR A 506 ARG 0.009 0.000 ARG A 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5456.43 seconds wall clock time: 101 minutes 1.93 seconds (6061.93 seconds total)