Starting phenix.real_space_refine on Thu Mar 21 07:26:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vav_31866/03_2024/7vav_31866_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vav_31866/03_2024/7vav_31866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vav_31866/03_2024/7vav_31866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vav_31866/03_2024/7vav_31866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vav_31866/03_2024/7vav_31866_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vav_31866/03_2024/7vav_31866_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18720 2.51 5 N 5125 2.21 5 O 5565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 164": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29520 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4476 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4467 Classifications: {'peptide': 577} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain breaks: 1 Chain: "C" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4476 Classifications: {'peptide': 578} Modifications used: {'COO': 1} 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: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 314 Classifications: {'peptide': 40} Modifications used: {'COO': 1} 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: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 314 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 981 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.69, per 1000 atoms: 0.57 Number of scatterers: 29520 At special positions: 0 Unit cell: (139.04, 176.88, 154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 5 15.00 Mg 2 11.99 O 5565 8.00 N 5125 7.00 C 18720 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: 12.77 Conformation dependent library (CDL) restraints added in 6.0 seconds 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6916 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 135 helices and 36 sheets defined 42.3% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.21 Creating SS restraints... Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 259 through 271 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 315 removed outlier: 4.082A pdb=" N GLU A 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.123A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 363 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 364 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 394 through 400 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 447 through 471 removed outlier: 3.842A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 532 Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.670A pdb=" N GLN A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.932A pdb=" N ARG A 552 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 574 removed outlier: 3.680A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 234 through 243 Processing helix chain 'B' and resid 259 through 271 Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 315 removed outlier: 4.645A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 341 Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.984A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 447 through 470 removed outlier: 3.999A pdb=" N GLN B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 478 through 493 Processing helix chain 'B' and resid 509 through 531 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 543 through 549 Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 559 through 577 removed outlier: 3.871A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 259 through 271 Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 296 through 315 removed outlier: 4.062A pdb=" N GLU C 300 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.848A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 394 through 401 removed outlier: 3.546A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 447 through 471 removed outlier: 4.292A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 475 No H-bonds generated for 'chain 'C' and resid 473 through 475' Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 509 through 531 Processing helix chain 'C' and resid 536 through 541 Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.632A pdb=" N GLY C 549 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG C 550 " --> pdb=" O ARG C 547 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG C 552 " --> pdb=" O GLY C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 577 removed outlier: 3.719A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 136 through 141 removed outlier: 3.576A pdb=" N MET D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 213 through 216 Processing helix chain 'D' and resid 228 through 249 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 287 through 297 removed outlier: 4.204A pdb=" N ARG D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 362 through 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.629A pdb=" N LEU D 395 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.862A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 450 No H-bonds generated for 'chain 'D' and resid 448 through 450' Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'D' and resid 470 through 472 No H-bonds generated for 'chain 'D' and resid 470 through 472' Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 228 through 249 removed outlier: 3.776A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 274 Processing helix chain 'E' and resid 285 through 297 removed outlier: 4.388A pdb=" N TYR E 288 " --> pdb=" O GLY E 285 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU E 296 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG E 297 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 324 through 330 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 362 through 365 No H-bonds generated for 'chain 'E' and resid 362 through 365' Processing helix chain 'E' and resid 375 through 399 removed outlier: 3.929A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 403 No H-bonds generated for 'chain 'E' and resid 401 through 403' Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 432 through 445 removed outlier: 4.056A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 458 through 461 No H-bonds generated for 'chain 'E' and resid 458 through 461' Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 228 through 249 removed outlier: 3.676A pdb=" N ARG F 231 " --> pdb=" O THR F 228 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.556A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS F 249 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 274 Processing helix chain 'F' and resid 287 through 297 removed outlier: 3.628A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ARG F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 345 Processing helix chain 'F' and resid 375 through 398 Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 406 through 421 Processing helix chain 'F' and resid 432 through 445 removed outlier: 3.886A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 456 through 462 Processing helix chain 'F' and resid 467 through 469 No H-bonds generated for 'chain 'F' and resid 467 through 469' Processing helix chain 'G' and resid 8 through 70 removed outlier: 3.760A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 111 through 114 Processing helix chain 'G' and resid 121 through 207 removed outlier: 3.894A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER G 127 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) removed outlier: 5.391A 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 7 through 15 Processing helix chain 'H' and resid 26 through 39 Processing helix chain 'H' and resid 55 through 58 Processing helix chain 'H' and resid 60 through 63 No H-bonds generated for 'chain 'H' and resid 60 through 63' Processing helix chain 'H' and resid 77 through 81 Processing helix chain 'H' and resid 86 through 98 Processing helix chain 'I' and resid 84 through 118 removed outlier: 3.541A pdb=" N ARG I 87 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET I 104 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA I 105 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU I 107 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASP I 108 " --> pdb=" O ALA I 105 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU I 109 " --> pdb=" O ARG I 106 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL I 118 " --> pdb=" O LEU I 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 92 Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 100 through 114 Processing helix chain 'J' and resid 128 through 130 No H-bonds generated for 'chain 'J' and resid 128 through 130' Processing helix chain 'J' and resid 132 through 137 Processing helix chain 'J' and resid 167 through 186 removed outlier: 4.290A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 118 removed outlier: 4.436A pdb=" N LEU K 85 " --> pdb=" O GLU K 82 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA K 86 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG K 87 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG K 106 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU K 107 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ASP K 108 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL K 118 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 96 Proline residue: L 95 - end of helix Processing helix chain 'L' and resid 100 through 114 Processing helix chain 'L' and resid 125 through 138 Proline residue: L 129 - end of helix removed outlier: 4.547A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 186 removed outlier: 4.779A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 6.560A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 Processing sheet with id= C, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.113A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 381 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 117 through 119 Processing sheet with id= E, first strand: chain 'A' and resid 366 through 369 Processing sheet with id= F, first strand: chain 'A' and resid 134 through 140 removed outlier: 6.687A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 157 through 160 removed outlier: 7.003A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 35 through 38 removed outlier: 6.709A pdb=" N ILE B 15 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE B 9 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ALA B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 72 through 76 Processing sheet with id= J, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.538A pdb=" N GLY B 164 " --> pdb=" O TRP B 119 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 138 through 140 Processing sheet with id= L, first strand: chain 'B' and resid 405 through 407 removed outlier: 8.491A pdb=" N ALA B 224 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE B 380 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE B 226 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY B 382 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 366 through 369 Processing sheet with id= N, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.982A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.647A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 72 through 76 Processing sheet with id= Q, first strand: chain 'C' and resid 117 through 119 Processing sheet with id= R, first strand: chain 'C' and resid 223 through 227 removed outlier: 8.641A pdb=" N ALA C 224 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE C 380 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE C 226 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY C 382 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL C 249 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N MET C 323 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C 251 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 366 through 369 Processing sheet with id= T, first strand: chain 'C' and resid 134 through 140 removed outlier: 6.682A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.913A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 10 through 15 removed outlier: 4.500A pdb=" N GLY D 10 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL D 73 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.712A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.947A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= Z, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.721A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= AB, first strand: chain 'E' and resid 217 through 221 removed outlier: 8.611A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N HIS E 252 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.532A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL F 73 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.635A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AF, first strand: chain 'F' and resid 217 through 220 removed outlier: 6.668A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 89 through 96 Processing sheet with id= AH, first strand: chain 'H' and resid 19 through 22 Processing sheet with id= AI, first strand: chain 'J' and resid 141 through 144 removed outlier: 3.769A pdb=" N GLU J 141 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 141 through 144 removed outlier: 3.618A pdb=" N ALA L 120 " --> pdb=" O VAL L 155 " (cutoff:3.500A) 1220 hydrogen bonds defined for protein. 3186 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: 10.22 Time building geometry restraints manager: 13.89 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: 9941 1.34 - 1.46: 3778 1.46 - 1.57: 16152 1.57 - 1.69: 9 1.69 - 1.81: 194 Bond restraints: 30074 Sorted by residual: bond pdb=" C4 ADP A 601 " pdb=" C5 ADP A 601 " ideal model delta sigma weight residual 1.490 1.386 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C5 ADP A 601 " pdb=" C6 ADP A 601 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" O3B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.592 -0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C8 ADP A 601 " pdb=" N7 ADP A 601 " ideal model delta sigma weight residual 1.350 1.310 0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" C5 ADP A 601 " pdb=" N7 ADP A 601 " ideal model delta sigma weight residual 1.350 1.387 -0.037 2.00e-02 2.50e+03 3.41e+00 ... (remaining 30069 not shown) Histogram of bond angle deviations from ideal: 100.11 - 108.06: 1279 108.06 - 116.01: 18576 116.01 - 123.96: 20195 123.96 - 131.91: 663 131.91 - 139.86: 41 Bond angle restraints: 40754 Sorted by residual: angle pdb=" PA ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 120.50 136.75 -16.25 3.00e+00 1.11e-01 2.93e+01 angle pdb=" O2B ADP A 601 " pdb=" PB ADP A 601 " pdb=" O3B ADP A 601 " ideal model delta sigma weight residual 119.90 107.25 12.65 3.00e+00 1.11e-01 1.78e+01 angle pdb=" C GLY G 118 " pdb=" N THR G 119 " pdb=" CA THR G 119 " ideal model delta sigma weight residual 120.06 124.95 -4.89 1.19e+00 7.06e-01 1.69e+01 angle pdb=" C GLY D 116 " pdb=" N LEU D 117 " pdb=" CA LEU D 117 " ideal model delta sigma weight residual 120.49 126.23 -5.74 1.42e+00 4.96e-01 1.63e+01 angle pdb=" C1' ADP A 601 " pdb=" C2' ADP A 601 " pdb=" C3' ADP A 601 " ideal model delta sigma weight residual 111.00 101.48 9.52 3.00e+00 1.11e-01 1.01e+01 ... (remaining 40749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.47: 17826 29.47 - 58.93: 446 58.93 - 88.40: 70 88.40 - 117.87: 6 117.87 - 147.33: 1 Dihedral angle restraints: 18349 sinusoidal: 7531 harmonic: 10818 Sorted by residual: dihedral pdb=" O2A ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PA ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 87.33 -147.33 1 2.00e+01 2.50e-03 4.42e+01 dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 -164.27 104.27 1 2.00e+01 2.50e-03 2.99e+01 dihedral pdb=" CA ASP D 416 " pdb=" CB ASP D 416 " pdb=" CG ASP D 416 " pdb=" OD1 ASP D 416 " ideal model delta sinusoidal sigma weight residual -30.00 -88.50 58.50 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 18346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3137 0.034 - 0.068: 936 0.068 - 0.102: 335 0.102 - 0.136: 156 0.136 - 0.171: 3 Chirality restraints: 4567 Sorted by residual: chirality pdb=" C2' ADP A 601 " pdb=" C1' ADP A 601 " pdb=" C3' ADP A 601 " pdb=" O2' ADP A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CB THR D 107 " pdb=" CA THR D 107 " pdb=" OG1 THR D 107 " pdb=" CG2 THR D 107 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 4564 not shown) Planarity restraints: 5336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN L 124 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO L 125 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 125 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 125 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO B 229 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 323 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO D 324 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 324 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 324 " -0.023 5.00e-02 4.00e+02 ... (remaining 5333 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 210 2.61 - 3.18: 24918 3.18 - 3.75: 44794 3.75 - 4.33: 62215 4.33 - 4.90: 105838 Nonbonded interactions: 237975 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 2.035 2.170 nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 2.059 2.170 nonbonded pdb=" O2B ADP A 601 " pdb="MG MG A 602 " model vdw 2.103 2.170 nonbonded pdb=" OG SER H 25 " pdb=" OE1 GLU H 28 " model vdw 2.147 2.440 nonbonded pdb=" O LEU B 241 " pdb=" OG SER B 245 " model vdw 2.182 2.440 ... (remaining 237970 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 32 or resid 34 through 578)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 32 or resid 34 through 578)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 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: 16.240 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 81.550 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.170 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:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 : 0.002 0.104 30074 Z= 0.154 Angle : 0.495 16.247 40754 Z= 0.258 Chirality : 0.041 0.171 4567 Planarity : 0.004 0.046 5336 Dihedral : 13.378 147.334 11433 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % 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: 1.80 (0.14), residues: 3761 helix: 2.25 (0.14), residues: 1547 sheet: 0.49 (0.22), residues: 583 loop : 0.56 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 471 HIS 0.003 0.001 HIS C 283 PHE 0.014 0.001 PHE G 108 TYR 0.009 0.001 TYR E 383 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 581 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 HIS cc_start: 0.7583 (m-70) cc_final: 0.7290 (m-70) REVERT: A 166 TYR cc_start: 0.7948 (m-80) cc_final: 0.7585 (m-80) REVERT: A 180 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6074 (mm-30) REVERT: A 282 MET cc_start: 0.8076 (tpt) cc_final: 0.7833 (tpt) REVERT: A 391 MET cc_start: 0.8057 (mmt) cc_final: 0.7638 (mmt) REVERT: A 416 ARG cc_start: 0.7453 (ttm110) cc_final: 0.7089 (mtp-110) REVERT: A 441 GLU cc_start: 0.7765 (tp30) cc_final: 0.7471 (mp0) REVERT: A 481 ARG cc_start: 0.6053 (tpt-90) cc_final: 0.5634 (mtm180) REVERT: A 531 LYS cc_start: 0.6641 (mttm) cc_final: 0.6276 (mmmm) REVERT: A 538 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7074 (mt-10) REVERT: A 567 MET cc_start: 0.6765 (mmm) cc_final: 0.6478 (mmp) REVERT: B 127 ASP cc_start: 0.6910 (m-30) cc_final: 0.6706 (m-30) REVERT: B 144 THR cc_start: 0.8332 (m) cc_final: 0.7981 (t) REVERT: B 156 ARG cc_start: 0.6224 (ptm-80) cc_final: 0.5740 (ptp90) REVERT: B 176 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6705 (mt-10) REVERT: B 445 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7021 (tm-30) REVERT: B 455 SER cc_start: 0.6904 (t) cc_final: 0.6538 (m) REVERT: B 496 GLN cc_start: 0.7958 (tt0) cc_final: 0.7748 (mt0) REVERT: C 124 LYS cc_start: 0.7177 (mppt) cc_final: 0.6728 (mppt) REVERT: C 127 ASP cc_start: 0.7112 (m-30) cc_final: 0.6784 (m-30) REVERT: C 170 GLU cc_start: 0.7763 (tp30) cc_final: 0.7525 (tp30) REVERT: C 179 THR cc_start: 0.7558 (m) cc_final: 0.7194 (p) REVERT: C 220 MET cc_start: 0.7694 (mmt) cc_final: 0.7455 (tpt) REVERT: C 276 LYS cc_start: 0.7227 (mtpt) cc_final: 0.6965 (mmmm) REVERT: C 391 MET cc_start: 0.8439 (mmt) cc_final: 0.8146 (mmt) REVERT: C 478 ASP cc_start: 0.6258 (m-30) cc_final: 0.5947 (m-30) REVERT: C 525 GLU cc_start: 0.6691 (mm-30) cc_final: 0.6096 (mt-10) REVERT: C 546 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6294 (tt0) REVERT: C 571 GLN cc_start: 0.6518 (pp30) cc_final: 0.6186 (tp40) REVERT: D 67 ASP cc_start: 0.7556 (p0) cc_final: 0.7251 (p0) REVERT: D 280 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7296 (mtp85) REVERT: D 452 LYS cc_start: 0.7899 (mttp) cc_final: 0.7606 (mmpt) REVERT: E 26 ASP cc_start: 0.7772 (m-30) cc_final: 0.7332 (t0) REVERT: E 136 SER cc_start: 0.8528 (m) cc_final: 0.8245 (t) REVERT: E 175 PRO cc_start: 0.7063 (Cg_endo) cc_final: 0.6817 (Cg_exo) REVERT: E 413 GLN cc_start: 0.5154 (pt0) cc_final: 0.4933 (tp40) REVERT: E 437 GLN cc_start: 0.7613 (tt0) cc_final: 0.7318 (tm-30) REVERT: F 15 SER cc_start: 0.8373 (t) cc_final: 0.7955 (p) REVERT: F 98 LYS cc_start: 0.7689 (mmtm) cc_final: 0.7239 (ttpp) REVERT: F 210 ARG cc_start: 0.7147 (ttp80) cc_final: 0.6696 (mtm110) REVERT: F 230 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7559 (mt-10) REVERT: F 296 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7841 (mm-30) REVERT: F 362 MET cc_start: 0.8361 (ttt) cc_final: 0.8137 (ttp) REVERT: G 92 GLU cc_start: 0.2111 (mt-10) cc_final: 0.1463 (mp0) REVERT: G 152 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7394 (pp20) REVERT: G 185 GLN cc_start: 0.7155 (tp40) cc_final: 0.6939 (tp40) REVERT: G 200 LYS cc_start: 0.6508 (mttp) cc_final: 0.6272 (mmmt) REVERT: J 141 GLU cc_start: 0.6112 (tt0) cc_final: 0.5751 (tp30) REVERT: J 160 LYS cc_start: 0.7158 (mmtp) cc_final: 0.6912 (mtmt) REVERT: J 173 ARG cc_start: 0.4744 (ttm-80) cc_final: 0.3540 (ttp80) REVERT: L 145 GLU cc_start: 0.4229 (tp30) cc_final: 0.3818 (mt-10) outliers start: 0 outliers final: 0 residues processed: 581 average time/residue: 1.8071 time to fit residues: 1185.2922 Evaluate side-chains 291 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 2.876 ------------------------------------------------------------------------------- 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: 8.9990 chunk 156 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 292 optimal weight: 0.0870 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 217 optimal weight: 9.9990 chunk 338 optimal weight: 30.0000 overall best weight: 7.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 7 GLN B 469 GLN D 206 GLN E 262 ASN E 338 GLN E 407 ASN F 310 GLN F 413 GLN G 180 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS J 162 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 30074 Z= 0.574 Angle : 0.773 10.500 40754 Z= 0.400 Chirality : 0.052 0.246 4567 Planarity : 0.007 0.079 5336 Dihedral : 6.232 115.284 4230 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.31 % Allowed : 10.22 % Favored : 86.47 % 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: 0.36 (0.14), residues: 3761 helix: 0.85 (0.13), residues: 1550 sheet: -0.00 (0.22), residues: 566 loop : -0.13 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 119 HIS 0.015 0.002 HIS B 283 PHE 0.018 0.003 PHE A 406 TYR 0.023 0.003 TYR G 133 ARG 0.013 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 279 time to evaluate : 3.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7110 (tmt90) REVERT: A 109 HIS cc_start: 0.7487 (m-70) cc_final: 0.7210 (m-70) REVERT: A 180 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6151 (mm-30) REVERT: A 241 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8662 (mt) REVERT: A 282 MET cc_start: 0.8000 (tpt) cc_final: 0.7742 (tpt) REVERT: A 294 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7623 (mmt) REVERT: A 441 GLU cc_start: 0.7890 (tp30) cc_final: 0.7492 (mp0) REVERT: A 481 ARG cc_start: 0.6318 (tpt-90) cc_final: 0.5800 (mtm110) REVERT: A 518 MET cc_start: 0.7554 (mtp) cc_final: 0.7336 (mtp) REVERT: A 531 LYS cc_start: 0.6501 (mttm) cc_final: 0.6175 (mmmm) REVERT: A 538 GLU cc_start: 0.7582 (mt-10) cc_final: 0.6911 (mt-10) REVERT: B 127 ASP cc_start: 0.7263 (m-30) cc_final: 0.6912 (m-30) REVERT: B 176 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7091 (mt-10) REVERT: B 340 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6730 (ttt180) REVERT: B 436 ASP cc_start: 0.6491 (m-30) cc_final: 0.6231 (m-30) REVERT: B 445 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7120 (tm-30) REVERT: B 459 GLN cc_start: 0.7474 (tm-30) cc_final: 0.7154 (mm110) REVERT: B 460 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6974 (ttp80) REVERT: B 496 GLN cc_start: 0.8229 (tt0) cc_final: 0.7823 (mt0) REVERT: C 124 LYS cc_start: 0.7343 (mppt) cc_final: 0.6782 (mptt) REVERT: C 127 ASP cc_start: 0.7735 (m-30) cc_final: 0.7300 (m-30) REVERT: C 133 MET cc_start: 0.7641 (mtp) cc_final: 0.7145 (mtp) REVERT: C 169 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7533 (mm-30) REVERT: C 170 GLU cc_start: 0.7944 (tp30) cc_final: 0.7660 (tp30) REVERT: C 179 THR cc_start: 0.7773 (m) cc_final: 0.7554 (p) REVERT: C 336 GLU cc_start: 0.7372 (tp30) cc_final: 0.6884 (tp30) REVERT: C 344 MET cc_start: 0.8435 (ttm) cc_final: 0.7988 (ttp) REVERT: C 491 ARG cc_start: 0.7722 (mtm110) cc_final: 0.7445 (ttp-110) REVERT: C 525 GLU cc_start: 0.6728 (mm-30) cc_final: 0.6218 (mt-10) REVERT: C 546 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6598 (tm-30) REVERT: D 67 ASP cc_start: 0.8092 (p0) cc_final: 0.7851 (p0) REVERT: D 265 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: D 280 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7531 (mtp-110) REVERT: D 388 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.7210 (t0) REVERT: D 452 LYS cc_start: 0.7982 (mttp) cc_final: 0.7688 (mmtt) REVERT: E 248 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: E 305 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7614 (mptp) REVERT: E 437 GLN cc_start: 0.7618 (tt0) cc_final: 0.7284 (tm-30) REVERT: F 15 SER cc_start: 0.8567 (t) cc_final: 0.8281 (p) REVERT: F 98 LYS cc_start: 0.7889 (mmtm) cc_final: 0.7317 (mtpp) REVERT: F 228 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8595 (m) REVERT: F 251 TYR cc_start: 0.8554 (m-80) cc_final: 0.8148 (m-80) REVERT: F 362 MET cc_start: 0.8549 (ttt) cc_final: 0.8339 (ttp) REVERT: F 420 ARG cc_start: 0.7438 (ttp80) cc_final: 0.7203 (ttm110) REVERT: G 92 GLU cc_start: 0.2187 (mt-10) cc_final: 0.1890 (mp0) REVERT: I 104 MET cc_start: 0.1064 (mmp) cc_final: 0.0788 (ptt) REVERT: J 160 LYS cc_start: 0.7102 (mmtp) cc_final: 0.6846 (mtmt) REVERT: L 138 ARG cc_start: 0.5124 (mmm160) cc_final: 0.4820 (mmp-170) REVERT: L 149 ARG cc_start: 0.4713 (OUTLIER) cc_final: 0.3999 (ttp-110) REVERT: L 168 LEU cc_start: 0.5834 (mt) cc_final: 0.5392 (tm) outliers start: 102 outliers final: 34 residues processed: 349 average time/residue: 1.7255 time to fit residues: 685.5543 Evaluate side-chains 273 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain J residue 113 GLU Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain J residue 176 ASP Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 149 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 281 optimal weight: 0.8980 chunk 230 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 339 optimal weight: 10.0000 chunk 366 optimal weight: 7.9990 chunk 302 optimal weight: 0.9980 chunk 336 optimal weight: 0.0050 chunk 115 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN A 498 ASN B 260 ASN C 571 GLN D 206 GLN G 180 GLN G 185 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30074 Z= 0.145 Angle : 0.503 7.938 40754 Z= 0.260 Chirality : 0.042 0.233 4567 Planarity : 0.005 0.054 5336 Dihedral : 5.345 90.632 4230 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.17 % Allowed : 12.43 % Favored : 85.40 % 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: 0.79 (0.14), residues: 3761 helix: 1.26 (0.14), residues: 1561 sheet: 0.13 (0.22), residues: 552 loop : 0.09 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 119 HIS 0.004 0.001 HIS B 283 PHE 0.010 0.001 PHE C 230 TYR 0.015 0.001 TYR G 133 ARG 0.006 0.000 ARG C 547 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 258 time to evaluate : 3.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 HIS cc_start: 0.7447 (m-70) cc_final: 0.7164 (m-70) REVERT: A 122 MET cc_start: 0.7195 (mtp) cc_final: 0.6432 (tmm) REVERT: A 180 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6229 (mm-30) REVERT: A 282 MET cc_start: 0.7933 (tpt) cc_final: 0.7655 (tpt) REVERT: A 441 GLU cc_start: 0.7881 (tp30) cc_final: 0.7485 (mp0) REVERT: A 481 ARG cc_start: 0.6091 (tpt-90) cc_final: 0.5666 (mtt180) REVERT: A 518 MET cc_start: 0.7605 (mtp) cc_final: 0.7367 (mtp) REVERT: A 538 GLU cc_start: 0.7631 (mt-10) cc_final: 0.6962 (mt-10) REVERT: B 127 ASP cc_start: 0.7137 (m-30) cc_final: 0.6862 (m-30) REVERT: B 165 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6553 (mt-10) REVERT: B 340 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6890 (ttm-80) REVERT: B 445 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7072 (tm-30) REVERT: B 455 SER cc_start: 0.6977 (t) cc_final: 0.6648 (m) REVERT: B 496 GLN cc_start: 0.8173 (tt0) cc_final: 0.7789 (mt0) REVERT: C 124 LYS cc_start: 0.7326 (mppt) cc_final: 0.6896 (mptt) REVERT: C 127 ASP cc_start: 0.7505 (m-30) cc_final: 0.7145 (m-30) REVERT: C 169 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7462 (mm-30) REVERT: C 170 GLU cc_start: 0.7839 (tp30) cc_final: 0.7637 (tp30) REVERT: C 179 THR cc_start: 0.7749 (m) cc_final: 0.7540 (p) REVERT: C 220 MET cc_start: 0.7553 (tpp) cc_final: 0.7255 (tpt) REVERT: C 336 GLU cc_start: 0.7337 (tp30) cc_final: 0.6848 (tp30) REVERT: C 344 MET cc_start: 0.8357 (ttm) cc_final: 0.8015 (ttp) REVERT: C 478 ASP cc_start: 0.6416 (m-30) cc_final: 0.5874 (m-30) REVERT: C 491 ARG cc_start: 0.7714 (mtm110) cc_final: 0.7389 (ttp-110) REVERT: C 525 GLU cc_start: 0.6620 (mm-30) cc_final: 0.6088 (mt-10) REVERT: C 546 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6569 (tm-30) REVERT: C 557 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: C 558 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6669 (pt0) REVERT: C 571 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6533 (mm-40) REVERT: D 67 ASP cc_start: 0.8057 (p0) cc_final: 0.7790 (p0) REVERT: D 162 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6922 (tt0) REVERT: D 237 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7868 (mtt) REVERT: D 265 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: D 280 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7435 (mtp-110) REVERT: D 452 LYS cc_start: 0.7978 (mttp) cc_final: 0.7657 (mmtt) REVERT: E 26 ASP cc_start: 0.7822 (m-30) cc_final: 0.7407 (t0) REVERT: E 287 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7928 (ttt) REVERT: E 305 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7720 (mptp) REVERT: E 362 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7479 (tpp) REVERT: E 437 GLN cc_start: 0.7637 (tt0) cc_final: 0.7291 (tm-30) REVERT: E 442 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.6008 (pt) REVERT: F 15 SER cc_start: 0.8471 (t) cc_final: 0.8125 (p) REVERT: F 78 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7066 (m-30) REVERT: F 98 LYS cc_start: 0.7822 (mmtm) cc_final: 0.7276 (ttpp) REVERT: F 199 ARG cc_start: 0.7718 (ttp80) cc_final: 0.7442 (mtm110) REVERT: F 228 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8513 (m) REVERT: F 251 TYR cc_start: 0.8447 (m-80) cc_final: 0.7870 (m-80) REVERT: G 159 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6629 (ptm160) REVERT: H 1 MET cc_start: 0.0713 (OUTLIER) cc_final: -0.0693 (ppp) REVERT: J 110 GLU cc_start: 0.5028 (tp30) cc_final: 0.4666 (mm-30) REVERT: J 113 GLU cc_start: 0.4477 (OUTLIER) cc_final: 0.3952 (pp20) REVERT: J 173 ARG cc_start: 0.4842 (ttm-80) cc_final: 0.3679 (ttp80) REVERT: L 138 ARG cc_start: 0.4888 (mmm160) cc_final: 0.4584 (mmp-170) REVERT: L 145 GLU cc_start: 0.3353 (tp30) cc_final: 0.2904 (mt-10) REVERT: L 168 LEU cc_start: 0.5875 (mt) cc_final: 0.5379 (tm) outliers start: 67 outliers final: 16 residues processed: 302 average time/residue: 1.7377 time to fit residues: 599.4794 Evaluate side-chains 261 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 229 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 113 GLU Chi-restraints excluded: chain K residue 104 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 20.0000 chunk 255 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 161 optimal weight: 0.0030 chunk 227 optimal weight: 0.0000 chunk 340 optimal weight: 0.0970 chunk 360 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 322 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 206 GLN G 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30074 Z= 0.138 Angle : 0.475 7.530 40754 Z= 0.243 Chirality : 0.042 0.182 4567 Planarity : 0.004 0.057 5336 Dihedral : 4.972 85.733 4230 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.14 % Allowed : 13.50 % Favored : 84.36 % 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: 0.98 (0.14), residues: 3761 helix: 1.42 (0.14), residues: 1556 sheet: 0.18 (0.22), residues: 540 loop : 0.21 (0.16), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 119 HIS 0.002 0.001 HIS B 283 PHE 0.008 0.001 PHE A 406 TYR 0.012 0.001 TYR G 133 ARG 0.007 0.000 ARG F 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 248 time to evaluate : 3.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 HIS cc_start: 0.7406 (m-70) cc_final: 0.7157 (m-70) REVERT: A 180 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6283 (mm-30) REVERT: A 241 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8587 (mm) REVERT: A 282 MET cc_start: 0.7926 (tpt) cc_final: 0.7629 (tpt) REVERT: A 441 GLU cc_start: 0.7830 (tp30) cc_final: 0.7467 (mp0) REVERT: A 481 ARG cc_start: 0.6122 (tpt-90) cc_final: 0.5698 (mtm110) REVERT: A 518 MET cc_start: 0.7581 (mtp) cc_final: 0.7337 (mtp) REVERT: A 538 GLU cc_start: 0.7625 (mt-10) cc_final: 0.6940 (mt-10) REVERT: B 127 ASP cc_start: 0.7137 (m-30) cc_final: 0.6865 (m-30) REVERT: B 165 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6543 (mt-10) REVERT: B 340 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6911 (ttm-80) REVERT: B 445 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7047 (tm-30) REVERT: B 455 SER cc_start: 0.6995 (t) cc_final: 0.6580 (m) REVERT: B 459 GLN cc_start: 0.7475 (tm-30) cc_final: 0.7117 (mm110) REVERT: B 460 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6841 (ttp80) REVERT: B 496 GLN cc_start: 0.8119 (tt0) cc_final: 0.7751 (mt0) REVERT: C 124 LYS cc_start: 0.7343 (mppt) cc_final: 0.6922 (mptt) REVERT: C 127 ASP cc_start: 0.7494 (m-30) cc_final: 0.7126 (m-30) REVERT: C 169 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7478 (mm-30) REVERT: C 170 GLU cc_start: 0.7813 (tp30) cc_final: 0.7559 (tp30) REVERT: C 179 THR cc_start: 0.7735 (m) cc_final: 0.7533 (p) REVERT: C 220 MET cc_start: 0.7593 (tpp) cc_final: 0.7272 (tpt) REVERT: C 336 GLU cc_start: 0.7343 (tp30) cc_final: 0.6849 (tp30) REVERT: C 344 MET cc_start: 0.8299 (ttm) cc_final: 0.7970 (ttp) REVERT: C 478 ASP cc_start: 0.6338 (m-30) cc_final: 0.5793 (m-30) REVERT: C 524 LYS cc_start: 0.7301 (mmpt) cc_final: 0.6877 (tmmt) REVERT: C 525 GLU cc_start: 0.6601 (mm-30) cc_final: 0.6267 (mt-10) REVERT: C 546 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6555 (tm-30) REVERT: C 558 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6782 (pt0) REVERT: D 162 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6972 (mt-10) REVERT: D 265 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: D 280 ARG cc_start: 0.7867 (mtp85) cc_final: 0.7435 (mtp-110) REVERT: D 452 LYS cc_start: 0.7974 (mttp) cc_final: 0.7631 (mmtt) REVERT: E 26 ASP cc_start: 0.7753 (m-30) cc_final: 0.7404 (t0) REVERT: E 287 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7985 (ttt) REVERT: E 305 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7749 (mptp) REVERT: E 362 MET cc_start: 0.7812 (ttt) cc_final: 0.7512 (tpp) REVERT: E 437 GLN cc_start: 0.7651 (tt0) cc_final: 0.7325 (tm-30) REVERT: F 15 SER cc_start: 0.8472 (t) cc_final: 0.8156 (p) REVERT: F 78 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.7014 (m-30) REVERT: F 98 LYS cc_start: 0.7742 (mmtm) cc_final: 0.7192 (ttpp) REVERT: F 228 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8468 (m) REVERT: G 148 LYS cc_start: 0.6004 (mmmt) cc_final: 0.5715 (tppt) REVERT: G 159 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6618 (ptm160) REVERT: H 1 MET cc_start: 0.1300 (mtt) cc_final: -0.0317 (ppp) REVERT: J 110 GLU cc_start: 0.5198 (tp30) cc_final: 0.4827 (mm-30) REVERT: J 113 GLU cc_start: 0.4699 (OUTLIER) cc_final: 0.4156 (pp20) REVERT: J 161 THR cc_start: 0.7038 (OUTLIER) cc_final: 0.6718 (t) REVERT: J 173 ARG cc_start: 0.4797 (ttm-80) cc_final: 0.3731 (ttp80) REVERT: K 106 ARG cc_start: 0.4967 (ttm110) cc_final: 0.4471 (tpp80) REVERT: L 131 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6918 (tm) REVERT: L 168 LEU cc_start: 0.5849 (mt) cc_final: 0.5386 (tm) outliers start: 66 outliers final: 26 residues processed: 294 average time/residue: 1.6158 time to fit residues: 546.4269 Evaluate side-chains 267 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 227 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain J residue 113 GLU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain L residue 131 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 0.1980 chunk 204 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 268 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 307 optimal weight: 10.0000 chunk 249 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 184 optimal weight: 0.2980 chunk 323 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 206 GLN E 338 GLN G 180 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30074 Z= 0.263 Angle : 0.535 8.436 40754 Z= 0.274 Chirality : 0.044 0.190 4567 Planarity : 0.005 0.057 5336 Dihedral : 5.102 84.197 4230 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.95 % Allowed : 13.79 % Favored : 83.26 % 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: 0.80 (0.14), residues: 3761 helix: 1.31 (0.14), residues: 1555 sheet: 0.08 (0.22), residues: 555 loop : 0.08 (0.16), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 119 HIS 0.007 0.001 HIS B 283 PHE 0.011 0.002 PHE A 48 TYR 0.016 0.001 TYR G 133 ARG 0.007 0.000 ARG C 547 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 231 time to evaluate : 3.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 HIS cc_start: 0.7414 (m-70) cc_final: 0.7151 (m-70) REVERT: A 122 MET cc_start: 0.7284 (mtp) cc_final: 0.6488 (tmm) REVERT: A 180 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6322 (mm-30) REVERT: A 220 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7850 (ttp) REVERT: A 241 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8568 (mm) REVERT: A 257 GLU cc_start: 0.7006 (tp30) cc_final: 0.6384 (mm-30) REVERT: A 441 GLU cc_start: 0.7844 (tp30) cc_final: 0.7490 (mp0) REVERT: A 481 ARG cc_start: 0.6223 (tpt-90) cc_final: 0.5785 (mtm110) REVERT: A 518 MET cc_start: 0.7614 (mtp) cc_final: 0.7395 (mtp) REVERT: A 520 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7373 (mp) REVERT: A 531 LYS cc_start: 0.6824 (OUTLIER) cc_final: 0.6590 (mtmm) REVERT: A 538 GLU cc_start: 0.7664 (mt-10) cc_final: 0.6996 (mt-10) REVERT: B 127 ASP cc_start: 0.7207 (m-30) cc_final: 0.6911 (m-30) REVERT: B 156 ARG cc_start: 0.6888 (ptp-170) cc_final: 0.6585 (ptp-170) REVERT: B 165 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7095 (mm-30) REVERT: B 340 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6990 (ttm-80) REVERT: B 436 ASP cc_start: 0.6455 (m-30) cc_final: 0.6220 (m-30) REVERT: B 445 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7035 (tm-30) REVERT: B 455 SER cc_start: 0.7040 (t) cc_final: 0.6668 (m) REVERT: B 496 GLN cc_start: 0.8200 (tt0) cc_final: 0.7763 (mt0) REVERT: C 124 LYS cc_start: 0.7356 (mppt) cc_final: 0.6904 (mptt) REVERT: C 127 ASP cc_start: 0.7626 (m-30) cc_final: 0.7237 (m-30) REVERT: C 169 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7485 (mm-30) REVERT: C 220 MET cc_start: 0.7608 (tpp) cc_final: 0.7227 (tpt) REVERT: C 336 GLU cc_start: 0.7364 (tp30) cc_final: 0.6862 (tp30) REVERT: C 344 MET cc_start: 0.8369 (ttm) cc_final: 0.7909 (ttp) REVERT: C 478 ASP cc_start: 0.6432 (m-30) cc_final: 0.5841 (m-30) REVERT: C 524 LYS cc_start: 0.7321 (mmpt) cc_final: 0.6892 (tmmt) REVERT: C 525 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6311 (mt-10) REVERT: C 546 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6603 (tm-30) REVERT: C 558 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6795 (pt0) REVERT: D 265 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: D 280 ARG cc_start: 0.7946 (mtp85) cc_final: 0.7505 (mtp-110) REVERT: D 420 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6852 (tpp-160) REVERT: D 452 LYS cc_start: 0.7893 (mttp) cc_final: 0.7625 (mmtm) REVERT: E 26 ASP cc_start: 0.7870 (m-30) cc_final: 0.7358 (t0) REVERT: E 287 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7890 (ttt) REVERT: E 305 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7794 (mptp) REVERT: E 362 MET cc_start: 0.7834 (ttt) cc_final: 0.7522 (tpp) REVERT: E 437 GLN cc_start: 0.7672 (tt0) cc_final: 0.7346 (tm-30) REVERT: F 15 SER cc_start: 0.8495 (t) cc_final: 0.8203 (p) REVERT: F 199 ARG cc_start: 0.7778 (ttp80) cc_final: 0.7459 (mtm110) REVERT: F 228 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8503 (m) REVERT: G 159 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6656 (ptm160) REVERT: G 190 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: G 196 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6533 (ttm-80) REVERT: G 201 ILE cc_start: 0.6446 (OUTLIER) cc_final: 0.6176 (mp) REVERT: H 1 MET cc_start: 0.1370 (mtt) cc_final: -0.0349 (ppp) REVERT: J 110 GLU cc_start: 0.5231 (tp30) cc_final: 0.4939 (mm-30) REVERT: J 161 THR cc_start: 0.7045 (OUTLIER) cc_final: 0.6690 (t) REVERT: J 173 ARG cc_start: 0.4787 (ttm-80) cc_final: 0.3708 (ttp80) REVERT: K 106 ARG cc_start: 0.5080 (ttm110) cc_final: 0.4728 (tpp80) REVERT: L 168 LEU cc_start: 0.5877 (mt) cc_final: 0.5420 (tm) outliers start: 91 outliers final: 41 residues processed: 295 average time/residue: 1.6661 time to fit residues: 564.6844 Evaluate side-chains 279 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 221 time to evaluate : 3.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 196 ARG Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain J residue 161 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 1.9990 chunk 324 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 360 optimal weight: 0.0870 chunk 299 optimal weight: 0.3980 chunk 167 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 overall best weight: 1.6964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN G 180 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30074 Z= 0.174 Angle : 0.492 11.186 40754 Z= 0.250 Chirality : 0.042 0.174 4567 Planarity : 0.004 0.062 5336 Dihedral : 4.907 82.014 4230 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.24 % Allowed : 15.31 % Favored : 82.45 % 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: 0.92 (0.14), residues: 3761 helix: 1.41 (0.14), residues: 1556 sheet: 0.10 (0.22), residues: 559 loop : 0.14 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 119 HIS 0.004 0.001 HIS B 283 PHE 0.009 0.001 PHE A 48 TYR 0.014 0.001 TYR G 133 ARG 0.008 0.000 ARG C 547 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 240 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 HIS cc_start: 0.7408 (m-70) cc_final: 0.7148 (m-70) REVERT: A 122 MET cc_start: 0.7249 (mtp) cc_final: 0.6523 (tmm) REVERT: A 180 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6279 (mm-30) REVERT: A 220 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7805 (ttp) REVERT: A 241 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8579 (mm) REVERT: A 257 GLU cc_start: 0.6895 (tp30) cc_final: 0.6318 (mm-30) REVERT: A 441 GLU cc_start: 0.7881 (tp30) cc_final: 0.7512 (mp0) REVERT: A 481 ARG cc_start: 0.6190 (tpt-90) cc_final: 0.5740 (mtm110) REVERT: A 518 MET cc_start: 0.7581 (mtp) cc_final: 0.7368 (mtp) REVERT: A 520 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7459 (mp) REVERT: B 127 ASP cc_start: 0.7198 (m-30) cc_final: 0.6918 (m-30) REVERT: B 156 ARG cc_start: 0.6880 (ptp-170) cc_final: 0.6676 (ptt180) REVERT: B 165 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7139 (mm-30) REVERT: B 340 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6922 (ttm-80) REVERT: B 445 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7016 (tm-30) REVERT: B 455 SER cc_start: 0.6997 (t) cc_final: 0.6575 (m) REVERT: B 459 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7238 (mm110) REVERT: B 460 ARG cc_start: 0.7433 (ttp80) cc_final: 0.7129 (mtm180) REVERT: B 496 GLN cc_start: 0.8160 (tt0) cc_final: 0.7731 (mt0) REVERT: C 124 LYS cc_start: 0.7424 (mppt) cc_final: 0.6971 (mptt) REVERT: C 127 ASP cc_start: 0.7596 (m-30) cc_final: 0.7224 (m-30) REVERT: C 169 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7442 (mm-30) REVERT: C 220 MET cc_start: 0.7624 (tpp) cc_final: 0.7216 (tpt) REVERT: C 336 GLU cc_start: 0.7363 (tp30) cc_final: 0.6858 (tp30) REVERT: C 344 MET cc_start: 0.8341 (ttm) cc_final: 0.7917 (ttp) REVERT: C 478 ASP cc_start: 0.6355 (m-30) cc_final: 0.5763 (m-30) REVERT: C 524 LYS cc_start: 0.7338 (mmpt) cc_final: 0.6917 (tmmt) REVERT: C 525 GLU cc_start: 0.6631 (mm-30) cc_final: 0.6291 (mt-10) REVERT: C 546 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6633 (tm-30) REVERT: C 557 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: C 558 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6787 (pt0) REVERT: D 265 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: D 280 ARG cc_start: 0.7898 (mtp85) cc_final: 0.7457 (mtp-110) REVERT: D 420 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6841 (tpp-160) REVERT: D 452 LYS cc_start: 0.7914 (mttp) cc_final: 0.7634 (mmtm) REVERT: E 26 ASP cc_start: 0.7844 (m-30) cc_final: 0.7348 (t0) REVERT: E 287 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7925 (ttt) REVERT: E 305 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7774 (mptp) REVERT: E 362 MET cc_start: 0.7824 (ttt) cc_final: 0.7560 (tpp) REVERT: E 437 GLN cc_start: 0.7632 (tt0) cc_final: 0.7320 (tm-30) REVERT: F 15 SER cc_start: 0.8500 (t) cc_final: 0.8196 (p) REVERT: F 78 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7118 (m-30) REVERT: F 199 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7443 (mtm110) REVERT: F 228 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8474 (m) REVERT: G 159 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6692 (ptm160) REVERT: G 196 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6450 (ttm-80) REVERT: H 1 MET cc_start: 0.1229 (mtt) cc_final: -0.0439 (ppp) REVERT: J 110 GLU cc_start: 0.5233 (tp30) cc_final: 0.4764 (mm-30) REVERT: J 134 LEU cc_start: 0.4907 (tp) cc_final: 0.4460 (mt) REVERT: J 161 THR cc_start: 0.7070 (OUTLIER) cc_final: 0.6732 (t) REVERT: J 173 ARG cc_start: 0.4773 (ttm-80) cc_final: 0.3702 (ttp80) REVERT: K 106 ARG cc_start: 0.5045 (ttm110) cc_final: 0.4683 (tpp80) REVERT: L 168 LEU cc_start: 0.5909 (mt) cc_final: 0.5439 (tm) outliers start: 69 outliers final: 34 residues processed: 286 average time/residue: 1.6759 time to fit residues: 549.2538 Evaluate side-chains 270 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 220 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 196 ARG Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain J residue 161 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 263 optimal weight: 20.0000 chunk 204 optimal weight: 10.0000 chunk 303 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 359 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 219 optimal weight: 0.0170 chunk 165 optimal weight: 10.0000 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN B 477 GLN ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN E 407 ASN G 180 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 30074 Z= 0.371 Angle : 0.604 10.363 40754 Z= 0.310 Chirality : 0.046 0.195 4567 Planarity : 0.006 0.060 5336 Dihedral : 5.360 83.624 4230 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.28 % Allowed : 15.02 % Favored : 81.70 % 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: 0.49 (0.14), residues: 3761 helix: 1.10 (0.14), residues: 1550 sheet: -0.09 (0.22), residues: 581 loop : -0.14 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 119 HIS 0.009 0.001 HIS B 283 PHE 0.014 0.002 PHE C 143 TYR 0.021 0.002 TYR G 133 ARG 0.007 0.001 ARG C 547 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 236 time to evaluate : 3.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 HIS cc_start: 0.7436 (m-70) cc_final: 0.7189 (m-70) REVERT: A 122 MET cc_start: 0.7276 (mtp) cc_final: 0.6539 (tmm) REVERT: A 180 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6383 (mm-30) REVERT: A 257 GLU cc_start: 0.6909 (tp30) cc_final: 0.6354 (mm-30) REVERT: A 441 GLU cc_start: 0.7918 (tp30) cc_final: 0.7525 (mp0) REVERT: A 481 ARG cc_start: 0.6330 (tpt-90) cc_final: 0.5864 (mtm110) REVERT: A 518 MET cc_start: 0.7725 (mtp) cc_final: 0.7495 (mtp) REVERT: A 520 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7346 (mp) REVERT: A 531 LYS cc_start: 0.6835 (OUTLIER) cc_final: 0.6603 (mtmm) REVERT: A 547 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6298 (ttm110) REVERT: B 127 ASP cc_start: 0.7337 (m-30) cc_final: 0.7024 (m-30) REVERT: B 156 ARG cc_start: 0.6995 (ptp-170) cc_final: 0.6793 (ptt180) REVERT: B 165 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: B 340 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7067 (ttm-80) REVERT: B 436 ASP cc_start: 0.6479 (m-30) cc_final: 0.6231 (m-30) REVERT: B 445 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7077 (tm-30) REVERT: B 455 SER cc_start: 0.7028 (t) cc_final: 0.6604 (m) REVERT: B 459 GLN cc_start: 0.7518 (tm-30) cc_final: 0.7148 (mm110) REVERT: B 496 GLN cc_start: 0.8190 (tt0) cc_final: 0.7738 (mt0) REVERT: C 124 LYS cc_start: 0.7530 (mppt) cc_final: 0.6976 (mptt) REVERT: C 127 ASP cc_start: 0.7882 (m-30) cc_final: 0.7519 (m-30) REVERT: C 169 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7469 (mm-30) REVERT: C 336 GLU cc_start: 0.7380 (tp30) cc_final: 0.6873 (tp30) REVERT: C 344 MET cc_start: 0.8496 (ttm) cc_final: 0.8189 (ttp) REVERT: C 524 LYS cc_start: 0.7302 (mmpt) cc_final: 0.6865 (tmmt) REVERT: C 525 GLU cc_start: 0.6731 (mm-30) cc_final: 0.6388 (mt-10) REVERT: C 546 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6593 (tm-30) REVERT: C 558 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6815 (pt0) REVERT: D 185 GLU cc_start: 0.5427 (OUTLIER) cc_final: 0.4918 (mm-30) REVERT: D 265 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: D 280 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7531 (mtp-110) REVERT: D 287 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8000 (ttt) REVERT: D 420 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6844 (tpp-160) REVERT: D 452 LYS cc_start: 0.7912 (mttp) cc_final: 0.7649 (mmtt) REVERT: E 7 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7472 (mm-30) REVERT: E 26 ASP cc_start: 0.8015 (m-30) cc_final: 0.7368 (t0) REVERT: E 177 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7112 (mt) REVERT: E 248 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: E 287 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7807 (ttt) REVERT: E 305 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7802 (mptp) REVERT: E 362 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7498 (tpp) REVERT: E 437 GLN cc_start: 0.7617 (tt0) cc_final: 0.7277 (tm-30) REVERT: F 15 SER cc_start: 0.8572 (t) cc_final: 0.8336 (p) REVERT: F 199 ARG cc_start: 0.7831 (ttp80) cc_final: 0.7507 (mtm110) REVERT: G 74 GLU cc_start: 0.2370 (OUTLIER) cc_final: 0.2104 (pt0) REVERT: G 159 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6684 (ptm160) REVERT: H 1 MET cc_start: 0.1375 (mtt) cc_final: -0.0340 (ppp) REVERT: J 161 THR cc_start: 0.7025 (OUTLIER) cc_final: 0.6682 (t) REVERT: J 173 ARG cc_start: 0.4862 (ttm-80) cc_final: 0.3773 (ttp80) outliers start: 101 outliers final: 42 residues processed: 309 average time/residue: 1.6682 time to fit residues: 592.9663 Evaluate side-chains 280 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 219 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain J residue 161 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 214 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 228 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 282 optimal weight: 0.0570 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN E 407 ASN G 180 GLN ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30074 Z= 0.145 Angle : 0.493 10.457 40754 Z= 0.249 Chirality : 0.042 0.198 4567 Planarity : 0.004 0.062 5336 Dihedral : 4.848 80.013 4230 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.75 % Allowed : 17.16 % Favored : 81.08 % 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: 0.87 (0.14), residues: 3761 helix: 1.39 (0.14), residues: 1551 sheet: 0.09 (0.22), residues: 545 loop : 0.09 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 119 HIS 0.002 0.001 HIS C 283 PHE 0.009 0.001 PHE C 230 TYR 0.013 0.001 TYR G 133 ARG 0.008 0.000 ARG C 547 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 236 time to evaluate : 3.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 HIS cc_start: 0.7412 (m-70) cc_final: 0.7170 (m-70) REVERT: A 122 MET cc_start: 0.7122 (mtp) cc_final: 0.6563 (tmm) REVERT: A 180 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6413 (mm-30) REVERT: A 257 GLU cc_start: 0.6801 (tp30) cc_final: 0.6180 (mm-30) REVERT: A 441 GLU cc_start: 0.7920 (tp30) cc_final: 0.7528 (mp0) REVERT: A 481 ARG cc_start: 0.6233 (tpt-90) cc_final: 0.5760 (mtm110) REVERT: A 518 MET cc_start: 0.7613 (mtp) cc_final: 0.7395 (mtp) REVERT: B 127 ASP cc_start: 0.7309 (m-30) cc_final: 0.7011 (m-30) REVERT: B 156 ARG cc_start: 0.6865 (ptp-170) cc_final: 0.6638 (ptt180) REVERT: B 165 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7107 (mm-30) REVERT: B 445 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7020 (tm-30) REVERT: B 455 SER cc_start: 0.6998 (t) cc_final: 0.6618 (m) REVERT: B 459 GLN cc_start: 0.7661 (tm-30) cc_final: 0.7302 (mm110) REVERT: B 496 GLN cc_start: 0.8079 (tt0) cc_final: 0.7710 (mt0) REVERT: C 124 LYS cc_start: 0.7577 (mppt) cc_final: 0.7069 (mptt) REVERT: C 127 ASP cc_start: 0.7646 (m-30) cc_final: 0.7275 (m-30) REVERT: C 169 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7470 (mm-30) REVERT: C 220 MET cc_start: 0.7512 (tpp) cc_final: 0.7192 (tpt) REVERT: C 336 GLU cc_start: 0.7389 (tp30) cc_final: 0.6877 (tp30) REVERT: C 344 MET cc_start: 0.8356 (ttm) cc_final: 0.8002 (ttp) REVERT: C 478 ASP cc_start: 0.6364 (m-30) cc_final: 0.5770 (m-30) REVERT: C 524 LYS cc_start: 0.7313 (mmpt) cc_final: 0.6886 (tmmt) REVERT: C 525 GLU cc_start: 0.6607 (mm-30) cc_final: 0.6191 (mt-10) REVERT: C 546 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6637 (tm-30) REVERT: C 557 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: C 558 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6853 (pt0) REVERT: D 265 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: D 280 ARG cc_start: 0.7912 (mtp85) cc_final: 0.7479 (mtp-110) REVERT: D 420 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6854 (tpp-160) REVERT: D 452 LYS cc_start: 0.7922 (mttp) cc_final: 0.7631 (mmtm) REVERT: E 26 ASP cc_start: 0.7873 (m-30) cc_final: 0.7406 (t0) REVERT: E 287 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7956 (ttt) REVERT: E 305 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7749 (mptp) REVERT: E 362 MET cc_start: 0.7820 (ttt) cc_final: 0.7581 (tpp) REVERT: E 437 GLN cc_start: 0.7579 (tt0) cc_final: 0.7276 (tm-30) REVERT: F 15 SER cc_start: 0.8492 (t) cc_final: 0.8223 (p) REVERT: G 74 GLU cc_start: 0.2073 (OUTLIER) cc_final: 0.1816 (pt0) REVERT: G 148 LYS cc_start: 0.6084 (mmmt) cc_final: 0.5791 (tppt) REVERT: G 159 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6649 (ptm160) REVERT: G 196 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6533 (ttm-80) REVERT: H 1 MET cc_start: 0.1268 (mtt) cc_final: -0.0423 (ppp) REVERT: J 110 GLU cc_start: 0.5405 (tp30) cc_final: 0.4904 (mm-30) REVERT: J 173 ARG cc_start: 0.4796 (ttm-80) cc_final: 0.3732 (ttp80) REVERT: L 168 LEU cc_start: 0.6069 (mt) cc_final: 0.5588 (tm) outliers start: 54 outliers final: 25 residues processed: 276 average time/residue: 1.7633 time to fit residues: 559.4227 Evaluate side-chains 253 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 218 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 196 ARG Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain L residue 89 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 1.9990 chunk 344 optimal weight: 9.9990 chunk 314 optimal weight: 10.0000 chunk 335 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 263 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 302 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 chunk 333 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN E 407 ASN G 180 GLN G 185 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 30074 Z= 0.474 Angle : 0.676 10.341 40754 Z= 0.346 Chirality : 0.049 0.203 4567 Planarity : 0.006 0.079 5336 Dihedral : 5.586 84.935 4230 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.14 % Allowed : 17.00 % Favored : 80.86 % 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: 0.15 (0.14), residues: 3761 helix: 0.87 (0.14), residues: 1542 sheet: -0.35 (0.21), residues: 603 loop : -0.35 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 100 HIS 0.011 0.002 HIS B 283 PHE 0.018 0.002 PHE E 418 TYR 0.025 0.002 TYR G 133 ARG 0.010 0.001 ARG E 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 222 time to evaluate : 3.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 HIS cc_start: 0.7432 (m-70) cc_final: 0.7191 (m-70) REVERT: A 122 MET cc_start: 0.7266 (mtp) cc_final: 0.6509 (tmm) REVERT: A 180 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6514 (mm-30) REVERT: A 257 GLU cc_start: 0.6883 (tp30) cc_final: 0.6332 (mm-30) REVERT: A 441 GLU cc_start: 0.7912 (tp30) cc_final: 0.7515 (mp0) REVERT: A 481 ARG cc_start: 0.6413 (tpt-90) cc_final: 0.5904 (mtm180) REVERT: A 518 MET cc_start: 0.7697 (mtp) cc_final: 0.7454 (mtp) REVERT: A 520 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7359 (mp) REVERT: B 127 ASP cc_start: 0.7448 (m-30) cc_final: 0.7096 (m-30) REVERT: B 165 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7069 (mm-30) REVERT: B 340 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7035 (ttm-80) REVERT: B 436 ASP cc_start: 0.6527 (m-30) cc_final: 0.6274 (m-30) REVERT: B 445 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7083 (tm-30) REVERT: B 459 GLN cc_start: 0.7534 (tm-30) cc_final: 0.7195 (mm110) REVERT: C 124 LYS cc_start: 0.7764 (mppt) cc_final: 0.7169 (mptt) REVERT: C 127 ASP cc_start: 0.7963 (m-30) cc_final: 0.7647 (m-30) REVERT: C 169 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7628 (mm-30) REVERT: C 220 MET cc_start: 0.7622 (tpp) cc_final: 0.7308 (tpt) REVERT: C 336 GLU cc_start: 0.7363 (tp30) cc_final: 0.6854 (tp30) REVERT: C 344 MET cc_start: 0.8537 (ttm) cc_final: 0.8132 (ttp) REVERT: C 524 LYS cc_start: 0.7346 (mmpt) cc_final: 0.6907 (tmmt) REVERT: C 525 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6383 (mt-10) REVERT: C 546 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6639 (tm-30) REVERT: C 558 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6819 (pt0) REVERT: D 185 GLU cc_start: 0.5387 (OUTLIER) cc_final: 0.4827 (mm-30) REVERT: D 265 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: D 280 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7586 (mtp-110) REVERT: D 420 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6367 (mpp-170) REVERT: D 452 LYS cc_start: 0.7944 (mttp) cc_final: 0.7704 (mmtt) REVERT: E 26 ASP cc_start: 0.8045 (m-30) cc_final: 0.7323 (t0) REVERT: E 287 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7777 (ttt) REVERT: E 305 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7801 (mptp) REVERT: E 362 MET cc_start: 0.7850 (ttt) cc_final: 0.7456 (tpp) REVERT: E 437 GLN cc_start: 0.7711 (tt0) cc_final: 0.7323 (tm-30) REVERT: F 15 SER cc_start: 0.8590 (t) cc_final: 0.8351 (p) REVERT: G 74 GLU cc_start: 0.2396 (OUTLIER) cc_final: 0.2155 (pt0) REVERT: G 148 LYS cc_start: 0.5915 (mmmt) cc_final: 0.5625 (tppt) REVERT: G 159 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6630 (ptm-80) REVERT: G 196 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6564 (ttm-80) REVERT: J 110 GLU cc_start: 0.5496 (tp30) cc_final: 0.4913 (mm-30) REVERT: J 173 ARG cc_start: 0.4916 (ttm-80) cc_final: 0.3827 (ttp80) REVERT: K 106 ARG cc_start: 0.5164 (ttm110) cc_final: 0.4862 (tpp80) outliers start: 66 outliers final: 33 residues processed: 272 average time/residue: 1.6388 time to fit residues: 511.6371 Evaluate side-chains 261 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 216 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 196 ARG Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 89 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 5.9990 chunk 354 optimal weight: 0.7980 chunk 216 optimal weight: 0.8980 chunk 168 optimal weight: 8.9990 chunk 246 optimal weight: 3.9990 chunk 371 optimal weight: 10.0000 chunk 342 optimal weight: 5.9990 chunk 295 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 228 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 ASN G 180 GLN G 185 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30074 Z= 0.204 Angle : 0.534 10.145 40754 Z= 0.271 Chirality : 0.043 0.216 4567 Planarity : 0.005 0.060 5336 Dihedral : 5.156 81.696 4230 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.56 % Allowed : 17.72 % Favored : 80.73 % 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: 0.54 (0.14), residues: 3761 helix: 1.20 (0.14), residues: 1542 sheet: -0.14 (0.22), residues: 580 loop : -0.15 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 119 HIS 0.005 0.001 HIS B 283 PHE 0.010 0.001 PHE G 130 TYR 0.019 0.001 TYR G 133 ARG 0.010 0.000 ARG C 547 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 221 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 HIS cc_start: 0.7430 (m-70) cc_final: 0.7188 (m-70) REVERT: A 122 MET cc_start: 0.7178 (mtp) cc_final: 0.6436 (tmm) REVERT: A 180 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6454 (mm-30) REVERT: A 257 GLU cc_start: 0.6805 (tp30) cc_final: 0.6284 (mm-30) REVERT: A 441 GLU cc_start: 0.7929 (tp30) cc_final: 0.7529 (mp0) REVERT: A 481 ARG cc_start: 0.6355 (tpt-90) cc_final: 0.5898 (mtm180) REVERT: A 518 MET cc_start: 0.7686 (mtp) cc_final: 0.7460 (mtp) REVERT: B 127 ASP cc_start: 0.7407 (m-30) cc_final: 0.7061 (m-30) REVERT: B 165 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7094 (mm-30) REVERT: B 340 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6958 (ttm-80) REVERT: B 436 ASP cc_start: 0.6523 (m-30) cc_final: 0.6287 (m-30) REVERT: B 445 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7087 (tm-30) REVERT: B 455 SER cc_start: 0.7025 (t) cc_final: 0.6575 (m) REVERT: B 459 GLN cc_start: 0.7633 (tm-30) cc_final: 0.7286 (mm110) REVERT: B 496 GLN cc_start: 0.8141 (tt0) cc_final: 0.7766 (mt0) REVERT: C 124 LYS cc_start: 0.7771 (mppt) cc_final: 0.7212 (mptt) REVERT: C 127 ASP cc_start: 0.7839 (m-30) cc_final: 0.7451 (m-30) REVERT: C 169 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7524 (mm-30) REVERT: C 220 MET cc_start: 0.7627 (tpp) cc_final: 0.7298 (tpt) REVERT: C 336 GLU cc_start: 0.7353 (tp30) cc_final: 0.6840 (tp30) REVERT: C 344 MET cc_start: 0.8470 (ttm) cc_final: 0.8093 (ttp) REVERT: C 416 ARG cc_start: 0.7239 (mtp-110) cc_final: 0.6946 (mmm-85) REVERT: C 524 LYS cc_start: 0.7295 (mmpt) cc_final: 0.6856 (tmmt) REVERT: C 525 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6315 (mt-10) REVERT: C 546 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6595 (tm-30) REVERT: C 558 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6784 (pt0) REVERT: D 265 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: D 280 ARG cc_start: 0.7892 (mtp85) cc_final: 0.7459 (mtp-110) REVERT: D 420 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6835 (tpp-160) REVERT: D 452 LYS cc_start: 0.7913 (mttp) cc_final: 0.7670 (mmtt) REVERT: E 26 ASP cc_start: 0.8018 (m-30) cc_final: 0.7384 (t0) REVERT: E 287 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7869 (ttt) REVERT: E 305 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7738 (mptp) REVERT: E 362 MET cc_start: 0.7876 (ttt) cc_final: 0.7662 (tpp) REVERT: E 437 GLN cc_start: 0.7646 (tt0) cc_final: 0.7278 (tm-30) REVERT: F 15 SER cc_start: 0.8485 (t) cc_final: 0.8217 (p) REVERT: F 199 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7438 (mtm110) REVERT: G 74 GLU cc_start: 0.2210 (OUTLIER) cc_final: 0.1973 (pt0) REVERT: G 148 LYS cc_start: 0.6005 (mmmt) cc_final: 0.5740 (tppt) REVERT: G 159 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6676 (ptm160) REVERT: G 196 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6590 (ttm-80) REVERT: H 1 MET cc_start: 0.1372 (mtt) cc_final: 0.1088 (ptp) REVERT: I 104 MET cc_start: 0.0713 (mmp) cc_final: 0.0272 (ptt) REVERT: J 110 GLU cc_start: 0.5339 (tp30) cc_final: 0.4905 (mm-30) REVERT: J 112 LEU cc_start: 0.5382 (mp) cc_final: 0.4975 (tt) REVERT: J 173 ARG cc_start: 0.4890 (ttm-80) cc_final: 0.3815 (ttp80) REVERT: L 168 LEU cc_start: 0.5948 (mt) cc_final: 0.5506 (tt) outliers start: 48 outliers final: 30 residues processed: 256 average time/residue: 1.6896 time to fit residues: 497.5893 Evaluate side-chains 256 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 216 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 196 ARG Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain L residue 89 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 10.0000 chunk 315 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 272 optimal weight: 0.0060 chunk 43 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 296 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 chunk 304 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN E 407 ASN G 180 GLN G 185 GLN ** H 82 GLN ** 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 = 0.3935 r_free = 0.3935 target = 0.135181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.104442 restraints weight = 50896.153| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.26 r_work: 0.3403 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30074 Z= 0.150 Angle : 0.497 10.306 40754 Z= 0.250 Chirality : 0.042 0.195 4567 Planarity : 0.004 0.061 5336 Dihedral : 4.792 79.448 4230 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.56 % Allowed : 17.81 % Favored : 80.63 % 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: 0.83 (0.14), residues: 3761 helix: 1.44 (0.14), residues: 1541 sheet: 0.01 (0.22), residues: 565 loop : 0.02 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 100 HIS 0.003 0.001 HIS B 283 PHE 0.010 0.001 PHE G 130 TYR 0.013 0.001 TYR G 133 ARG 0.010 0.000 ARG C 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10688.11 seconds wall clock time: 189 minutes 2.51 seconds (11342.51 seconds total)