Starting phenix.real_space_refine on Wed Feb 21 02:49:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vas_31861/02_2024/7vas_31861_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vas_31861/02_2024/7vas_31861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vas_31861/02_2024/7vas_31861.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vas_31861/02_2024/7vas_31861.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vas_31861/02_2024/7vas_31861_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vas_31861/02_2024/7vas_31861_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 5558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 558": "OE1" <-> "OE2" Residue "D TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 373": "OE1" <-> "OE2" Residue "F PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29513 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4466 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 35, 'TRANS': 541} Chain breaks: 1 Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} 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: 15.74, per 1000 atoms: 0.53 Number of scatterers: 29513 At special positions: 0 Unit cell: (139.04, 178.64, 151.36, 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 5558 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.81 Conformation dependent library (CDL) restraints added in 5.7 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: 133 helices and 36 sheets defined 41.5% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.93 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: 4.290A 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: 4.105A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A 363 " --> pdb=" O ALA A 360 " (cutoff:3.500A) 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: 4.026A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (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 Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.136A pdb=" N ARG A 552 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 577 removed outlier: 3.527A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.535A 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 244 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: 4.958A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.751A 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 416 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix removed outlier: 3.543A pdb=" N GLU B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 470 removed outlier: 3.640A pdb=" N GLN B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 469 " --> pdb=" O GLN B 465 " (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 532 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 572 Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' 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 268 Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 296 through 315 removed outlier: 4.104A 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: 3.950A 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 400 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 447 through 471 removed outlier: 4.148A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 470 " --> pdb=" O GLU C 466 " (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 532 Processing helix chain 'C' and resid 536 through 540 Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 551 through 553 No H-bonds generated for 'chain 'C' and resid 551 through 553' Processing helix chain 'C' and resid 559 through 577 removed outlier: 4.116A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS C 575 " --> pdb=" O GLN C 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 136 through 141 Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 175 through 178 No H-bonds generated for 'chain 'D' and resid 175 through 178' 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 274 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 295 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 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.831A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.246A 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: 3.895A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 462 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 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 198 through 211 Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 229 through 249 removed outlier: 3.755A pdb=" N THR E 234 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.579A pdb=" N PHE E 247 " --> pdb=" O TYR E 244 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU E 248 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS E 249 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 274 Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.650A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ARG E 297 " --> pdb=" O THR E 293 " (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: 3.971A 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: 3.866A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) 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 213 through 216 Processing helix chain 'F' and resid 230 through 249 removed outlier: 3.847A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.575A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS F 249 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 287 through 297 removed outlier: 3.689A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 5.144A 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: 3.916A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 462 Processing helix chain 'F' and resid 467 through 470 No H-bonds generated for 'chain 'F' and resid 467 through 470' Processing helix chain 'G' and resid 8 through 70 removed outlier: 3.517A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.691A 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 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 121 through 166 removed outlier: 3.707A pdb=" N GLU G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER G 127 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 208 Processing helix chain 'H' and resid 7 through 15 removed outlier: 3.798A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 55 through 58 No H-bonds generated for 'chain 'H' and resid 55 through 58' Processing helix chain 'H' and resid 77 through 80 No H-bonds generated for 'chain 'H' and resid 77 through 80' Processing helix chain 'H' and resid 86 through 98 Processing helix chain 'I' and resid 82 through 118 removed outlier: 3.751A pdb=" N GLU I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA I 110 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 93 Processing helix chain 'J' and resid 100 through 114 removed outlier: 4.062A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 136 removed outlier: 4.386A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ARG J 136 " --> pdb=" O GLU J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 170 through 186 removed outlier: 4.319A pdb=" N TRP J 175 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP J 176 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER J 179 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER J 180 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 118 removed outlier: 3.875A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA K 110 " --> pdb=" O ARG K 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 92 Processing helix chain 'L' and resid 94 through 96 No H-bonds generated for 'chain 'L' and resid 94 through 96' 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: 4.902A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA L 135 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 186 removed outlier: 4.743A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.546A 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: 6.553A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.698A 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: 4.076A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.662A 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 197 through 199 removed outlier: 3.737A pdb=" N ARG A 197 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS A 367 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 134 through 140 removed outlier: 6.721A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.552A 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: 6.953A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 3 through 5 removed outlier: 6.669A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 72 through 75 Processing sheet with id= J, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.082A pdb=" N GLY B 82 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B 250 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ILE B 288 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYR B 252 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA B 377 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU B 322 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR B 379 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ALA B 324 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL B 381 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA B 405 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N TRP B 407 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 366 through 369 Processing sheet with id= L, first strand: chain 'B' and resid 134 through 140 removed outlier: 6.630A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.974A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.587A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 72 through 76 Processing sheet with id= P, first strand: chain 'C' and resid 117 through 119 Processing sheet with id= Q, first strand: chain 'C' and resid 223 through 227 removed outlier: 8.582A pdb=" N ALA C 224 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE C 380 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE C 226 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY C 382 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 249 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N MET C 323 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL C 251 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 134 through 140 removed outlier: 6.517A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.973A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.425A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL D 73 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 81 through 84 Processing sheet with id= V, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= W, first strand: chain 'D' and resid 217 through 221 removed outlier: 8.845A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.503A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.079A pdb=" N PHE E 93 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU E 219 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ASN E 222 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ALA E 193 " --> pdb=" O ASN E 222 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 129 through 131 removed outlier: 4.702A pdb=" N GLN E 129 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (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 'F' and resid 11 through 15 removed outlier: 6.419A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.562A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 92 through 94 removed outlier: 8.090A pdb=" N PHE F 93 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU F 219 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (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 32 through 36 removed outlier: 3.538A pdb=" N GLU F 77 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL F 73 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 90 through 96 removed outlier: 3.518A pdb=" N GLU G 92 " --> pdb=" O ARG G 103 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 19 through 22 removed outlier: 3.633A pdb=" N LEU H 72 " --> pdb=" O VAL H 45 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 140 through 144 removed outlier: 3.822A pdb=" N VAL J 140 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY J 156 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU J 121 " --> pdb=" O ALA J 154 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ALA J 154 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 141 through 144 removed outlier: 3.664A pdb=" N GLN L 143 " --> pdb=" O LEU L 121 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA L 123 " --> pdb=" O GLN L 143 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA L 120 " --> pdb=" O VAL L 155 " (cutoff:3.500A) 1189 hydrogen bonds defined for protein. 3243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.51 Time building geometry restraints manager: 12.83 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: 9671 1.34 - 1.45: 3161 1.45 - 1.57: 17032 1.57 - 1.69: 9 1.69 - 1.81: 194 Bond restraints: 30067 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 2.72e+01 bond pdb=" C5 ADP A 601 " pdb=" C6 ADP A 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.589 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" N LEU H 44 " pdb=" CA LEU H 44 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.22e-02 6.72e+03 8.70e+00 bond pdb=" N THR B 46 " pdb=" CA THR B 46 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.59e+00 ... (remaining 30062 not shown) Histogram of bond angle deviations from ideal: 100.12 - 108.04: 1290 108.04 - 115.96: 18467 115.96 - 123.88: 20258 123.88 - 131.80: 683 131.80 - 139.72: 42 Bond angle restraints: 40740 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 120.50 136.76 -16.26 3.00e+00 1.11e-01 2.94e+01 angle pdb=" N GLY E 369 " pdb=" CA GLY E 369 " pdb=" C GLY E 369 " ideal model delta sigma weight residual 115.36 108.76 6.60 1.33e+00 5.65e-01 2.46e+01 angle pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " pdb=" O2B ADP A 601 " ideal model delta sigma weight residual 119.90 107.15 12.75 3.00e+00 1.11e-01 1.80e+01 angle pdb=" CA GLY F 426 " pdb=" C GLY F 426 " pdb=" O GLY F 426 " ideal model delta sigma weight residual 121.41 117.77 3.64 8.80e-01 1.29e+00 1.71e+01 angle pdb=" CA ASP B 43 " pdb=" C ASP B 43 " pdb=" O ASP B 43 " ideal model delta sigma weight residual 121.49 117.10 4.39 1.16e+00 7.43e-01 1.43e+01 ... (remaining 40735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.48: 17863 31.48 - 62.96: 432 62.96 - 94.44: 45 94.44 - 125.93: 1 125.93 - 157.41: 1 Dihedral angle restraints: 18342 sinusoidal: 7524 harmonic: 10818 Sorted by residual: 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 97.40 -157.41 1 2.00e+01 2.50e-03 4.62e+01 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 54.01 -114.01 1 2.00e+01 2.50e-03 3.38e+01 dihedral pdb=" CA LEU J 168 " pdb=" C LEU J 168 " pdb=" N ALA J 169 " pdb=" CA ALA J 169 " ideal model delta harmonic sigma weight residual -180.00 -151.30 -28.70 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 18339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4135 0.076 - 0.153: 424 0.153 - 0.229: 7 0.229 - 0.306: 0 0.306 - 0.382: 1 Chirality restraints: 4567 Sorted by residual: chirality pdb=" CA THR E 371 " pdb=" N THR E 371 " pdb=" C THR E 371 " pdb=" CB THR E 371 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA LYS E 370 " pdb=" N LYS E 370 " pdb=" C LYS E 370 " pdb=" CB LYS E 370 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA LEU H 44 " pdb=" N LEU H 44 " pdb=" C LEU H 44 " pdb=" CB LEU H 44 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 4564 not shown) Planarity restraints: 5329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 202 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C SER E 202 " 0.032 2.00e-02 2.50e+03 pdb=" O SER E 202 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR E 203 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 393 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 394 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 269 " -0.012 2.00e-02 2.50e+03 1.23e-02 2.64e+00 pdb=" CG PHE A 269 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 269 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 269 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 269 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 269 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 269 " -0.001 2.00e-02 2.50e+03 ... (remaining 5326 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 158 2.58 - 3.16: 23983 3.16 - 3.74: 44996 3.74 - 4.32: 62839 4.32 - 4.90: 107543 Nonbonded interactions: 239519 Sorted by model distance: nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 2.006 2.170 nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 2.026 2.170 nonbonded pdb=" CD2 LEU H 44 " pdb=" CG1 VAL H 70 " model vdw 2.038 3.880 nonbonded pdb=" O PRO A 386 " pdb=" OH TYR F 331 " model vdw 2.117 2.440 nonbonded pdb=" OG SER D 431 " pdb=" OE1 GLU D 433 " model vdw 2.176 2.440 ... (remaining 239514 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: 16.010 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: 0.000 Extract box with map and model: 9.820 Check model and map are aligned: 0.400 Set scattering table: 0.280 Process input model: 76.860 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.180 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:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 30067 Z= 0.220 Angle : 0.525 16.260 40740 Z= 0.275 Chirality : 0.043 0.382 4567 Planarity : 0.004 0.041 5329 Dihedral : 13.727 157.407 11426 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.13 % Allowed : 0.23 % Favored : 99.64 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.34 % 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: 1.38 (0.14), residues: 3761 helix: 2.08 (0.14), residues: 1543 sheet: 0.17 (0.22), residues: 580 loop : 0.15 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 119 HIS 0.003 0.001 HIS J 130 PHE 0.028 0.001 PHE A 269 TYR 0.010 0.001 TYR D 463 ARG 0.008 0.000 ARG J 153 *********************** 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 562 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 558 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8545 (mmm) cc_final: 0.8193 (mmm) REVERT: A 123 VAL cc_start: 0.8066 (m) cc_final: 0.7823 (p) REVERT: A 124 LYS cc_start: 0.7773 (mtmm) cc_final: 0.7156 (mtmm) REVERT: A 156 ARG cc_start: 0.6418 (ttp80) cc_final: 0.5563 (ttt180) REVERT: A 176 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6700 (mp0) REVERT: A 264 ASP cc_start: 0.7060 (m-30) cc_final: 0.6631 (m-30) REVERT: A 456 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6768 (mp0) REVERT: A 491 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6943 (mtt-85) REVERT: B 45 ASP cc_start: 0.7353 (t0) cc_final: 0.7067 (t0) REVERT: B 48 PHE cc_start: 0.8329 (m-80) cc_final: 0.8054 (m-80) REVERT: B 130 ARG cc_start: 0.6884 (ptp-110) cc_final: 0.6653 (pmm-80) REVERT: B 161 LYS cc_start: 0.8078 (mmtm) cc_final: 0.7869 (mptt) REVERT: B 274 ASP cc_start: 0.7978 (t70) cc_final: 0.7743 (t70) REVERT: B 326 SER cc_start: 0.8370 (m) cc_final: 0.8053 (p) REVERT: B 480 GLU cc_start: 0.7084 (mp0) cc_final: 0.6696 (mp0) REVERT: B 500 TYR cc_start: 0.8142 (m-80) cc_final: 0.7890 (m-10) REVERT: B 524 LYS cc_start: 0.8494 (ttpp) cc_final: 0.7870 (mmtp) REVERT: B 538 GLU cc_start: 0.7276 (tt0) cc_final: 0.6461 (tp30) REVERT: B 540 LEU cc_start: 0.7146 (mm) cc_final: 0.6800 (mm) REVERT: B 547 ARG cc_start: 0.7436 (mmm-85) cc_final: 0.6657 (tpp-160) REVERT: C 393 GLU cc_start: 0.7253 (tt0) cc_final: 0.7041 (tt0) REVERT: C 470 LEU cc_start: 0.7610 (mm) cc_final: 0.7256 (mt) REVERT: C 478 ASP cc_start: 0.6440 (m-30) cc_final: 0.5662 (t0) REVERT: C 481 ARG cc_start: 0.7912 (mtp180) cc_final: 0.7482 (mmm160) REVERT: C 537 ASP cc_start: 0.6536 (m-30) cc_final: 0.6047 (m-30) REVERT: D 77 GLU cc_start: 0.7780 (tt0) cc_final: 0.7347 (tt0) REVERT: D 128 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6618 (mt-10) REVERT: D 466 LYS cc_start: 0.7251 (tttp) cc_final: 0.6895 (mmtp) REVERT: E 6 LYS cc_start: 0.7772 (tttp) cc_final: 0.7021 (ptpt) REVERT: E 25 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7907 (mtmm) REVERT: E 67 ASP cc_start: 0.8168 (p0) cc_final: 0.7787 (p0) REVERT: E 196 ILE cc_start: 0.8110 (pt) cc_final: 0.7907 (tt) REVERT: E 216 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.7323 (ttm110) REVERT: E 401 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6689 (mp0) REVERT: E 420 ARG cc_start: 0.7466 (mmm160) cc_final: 0.7174 (mmm-85) REVERT: E 428 GLN cc_start: 0.8698 (mt0) cc_final: 0.8408 (mt0) REVERT: F 6 LYS cc_start: 0.8057 (tttt) cc_final: 0.7322 (ptpt) REVERT: F 7 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7355 (mt-10) REVERT: F 380 ASP cc_start: 0.7579 (m-30) cc_final: 0.7248 (m-30) REVERT: F 450 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7364 (mm-30) REVERT: G 19 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.7278 (ttt180) REVERT: G 48 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6679 (mt-10) REVERT: G 101 VAL cc_start: 0.7155 (p) cc_final: 0.6862 (p) REVERT: G 104 LEU cc_start: 0.6185 (mm) cc_final: 0.5968 (mt) REVERT: G 105 LYS cc_start: 0.4766 (tptp) cc_final: 0.3697 (ptmm) REVERT: G 146 ARG cc_start: 0.7137 (mtp180) cc_final: 0.6639 (ttp-170) REVERT: G 149 LYS cc_start: 0.7652 (mmtt) cc_final: 0.6940 (tptt) REVERT: G 153 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6879 (mm-30) REVERT: G 202 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6390 (tm-30) REVERT: H 56 GLU cc_start: 0.6773 (pt0) cc_final: 0.6032 (pm20) REVERT: H 60 GLU cc_start: 0.6993 (tt0) cc_final: 0.6178 (pp20) REVERT: J 74 GLN cc_start: 0.7303 (mm-40) cc_final: 0.6919 (mm-40) REVERT: J 76 ARG cc_start: 0.6315 (mtp85) cc_final: 0.5394 (mtt-85) REVERT: J 110 GLU cc_start: 0.6716 (mt-10) cc_final: 0.6342 (tp30) REVERT: J 162 GLN cc_start: 0.7861 (mt0) cc_final: 0.7145 (mp10) REVERT: J 179 SER cc_start: 0.8148 (t) cc_final: 0.7763 (m) REVERT: K 100 ARG cc_start: 0.6049 (ttm110) cc_final: 0.5273 (mtt180) REVERT: L 76 ARG cc_start: 0.6575 (mtp-110) cc_final: 0.6294 (mtm-85) REVERT: L 81 GLU cc_start: 0.6953 (tp30) cc_final: 0.6341 (mm-30) REVERT: L 84 ARG cc_start: 0.6128 (tpt-90) cc_final: 0.5354 (tmm160) REVERT: L 85 ARG cc_start: 0.6784 (ttp80) cc_final: 0.6033 (ttp-110) REVERT: L 86 ARG cc_start: 0.7104 (mtp85) cc_final: 0.6754 (mtm-85) REVERT: L 105 ARG cc_start: 0.6423 (mtm180) cc_final: 0.6205 (mtm-85) REVERT: L 138 ARG cc_start: 0.6511 (mmm160) cc_final: 0.6268 (ttm110) REVERT: L 141 GLU cc_start: 0.6002 (tt0) cc_final: 0.5786 (tp30) REVERT: L 149 ARG cc_start: 0.7127 (ttm110) cc_final: 0.6188 (mtm110) outliers start: 4 outliers final: 2 residues processed: 562 average time/residue: 1.9303 time to fit residues: 1220.7527 Evaluate side-chains 309 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 307 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain H residue 33 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 6.9990 chunk 282 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 190 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 292 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 chunk 338 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN B 541 GLN C 316 GLN C 459 GLN C 541 GLN D 363 ASN D 407 ASN D 448 GLN E 166 GLN E 170 GLN E 206 GLN E 413 GLN F 170 GLN F 425 GLN F 437 GLN G 181 GLN L 130 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 30067 Z= 0.384 Angle : 0.614 7.411 40740 Z= 0.317 Chirality : 0.047 0.176 4567 Planarity : 0.006 0.061 5329 Dihedral : 6.122 158.574 4226 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.24 % Allowed : 9.67 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.82 (0.14), residues: 3761 helix: 1.50 (0.14), residues: 1534 sheet: 0.06 (0.23), residues: 541 loop : -0.09 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 100 HIS 0.007 0.001 HIS C 283 PHE 0.031 0.002 PHE A 269 TYR 0.019 0.002 TYR H 42 ARG 0.007 0.001 ARG C 130 *********************** 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 371 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 302 time to evaluate : 3.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.7812 (mtmm) cc_final: 0.7386 (mtmm) REVERT: A 130 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6359 (mtp85) REVERT: A 133 MET cc_start: 0.7812 (mtt) cc_final: 0.7550 (mtt) REVERT: A 176 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6700 (mp0) REVERT: A 456 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6712 (mp0) REVERT: A 491 ARG cc_start: 0.7382 (mtm-85) cc_final: 0.7074 (mtt-85) REVERT: B 45 ASP cc_start: 0.7411 (t0) cc_final: 0.6958 (t70) REVERT: B 48 PHE cc_start: 0.8299 (m-80) cc_final: 0.8095 (m-80) REVERT: B 62 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7218 (mt-10) REVERT: B 130 ARG cc_start: 0.7113 (ptp-110) cc_final: 0.6758 (mtt-85) REVERT: B 176 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6775 (mt-10) REVERT: B 500 TYR cc_start: 0.8155 (m-80) cc_final: 0.7933 (m-10) REVERT: B 524 LYS cc_start: 0.8487 (ttpp) cc_final: 0.7901 (mmtp) REVERT: B 538 GLU cc_start: 0.7130 (tt0) cc_final: 0.6192 (tp30) REVERT: B 547 ARG cc_start: 0.7523 (mmm-85) cc_final: 0.6746 (tpp-160) REVERT: C 114 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7312 (mm-30) REVERT: C 481 ARG cc_start: 0.7880 (mtp180) cc_final: 0.7531 (mmm160) REVERT: C 525 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: D 77 GLU cc_start: 0.7609 (tt0) cc_final: 0.7218 (tt0) REVERT: D 128 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6813 (mt-10) REVERT: D 373 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.7025 (pt0) REVERT: D 466 LYS cc_start: 0.7589 (tttp) cc_final: 0.6881 (mmtp) REVERT: E 6 LYS cc_start: 0.7782 (tttp) cc_final: 0.6937 (ptpt) REVERT: E 25 LYS cc_start: 0.8464 (mtmm) cc_final: 0.8020 (mttm) REVERT: E 67 ASP cc_start: 0.8303 (p0) cc_final: 0.7941 (p0) REVERT: E 274 ARG cc_start: 0.7457 (mmm160) cc_final: 0.6683 (mtp180) REVERT: E 391 ASP cc_start: 0.7630 (p0) cc_final: 0.7407 (p0) REVERT: E 401 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6613 (mp0) REVERT: E 420 ARG cc_start: 0.7628 (mmm160) cc_final: 0.7253 (mmm-85) REVERT: E 428 GLN cc_start: 0.8631 (mt0) cc_final: 0.8342 (mt0) REVERT: F 6 LYS cc_start: 0.8169 (tttt) cc_final: 0.7348 (ptpt) REVERT: F 7 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7268 (mt-10) REVERT: F 380 ASP cc_start: 0.7694 (m-30) cc_final: 0.7390 (m-30) REVERT: F 450 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7472 (mm-30) REVERT: G 9 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7318 (ptm) REVERT: G 48 GLU cc_start: 0.6890 (tm-30) cc_final: 0.6677 (mt-10) REVERT: G 105 LYS cc_start: 0.4532 (tptp) cc_final: 0.3527 (ptmm) REVERT: G 146 ARG cc_start: 0.7262 (mtp180) cc_final: 0.6756 (ttm170) REVERT: G 149 LYS cc_start: 0.7701 (mmtt) cc_final: 0.7027 (mmmt) REVERT: G 153 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6904 (mm-30) REVERT: G 202 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6421 (tm-30) REVERT: H 56 GLU cc_start: 0.6882 (pt0) cc_final: 0.6008 (pm20) REVERT: H 92 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7806 (tt0) REVERT: J 110 GLU cc_start: 0.6619 (mt-10) cc_final: 0.6211 (tp30) REVERT: J 150 LEU cc_start: 0.5825 (OUTLIER) cc_final: 0.5419 (mp) REVERT: J 162 GLN cc_start: 0.7923 (mt0) cc_final: 0.7183 (mp10) REVERT: K 100 ARG cc_start: 0.6074 (ttm110) cc_final: 0.5251 (mtt180) REVERT: K 101 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6790 (mm-30) REVERT: L 81 GLU cc_start: 0.6857 (tp30) cc_final: 0.6218 (mm-30) REVERT: L 82 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.5919 (tm-30) REVERT: L 85 ARG cc_start: 0.6735 (ttp80) cc_final: 0.5629 (ttm170) REVERT: L 105 ARG cc_start: 0.6538 (mtm180) cc_final: 0.6314 (mtm-85) REVERT: L 138 ARG cc_start: 0.6529 (mmm160) cc_final: 0.6283 (ttm110) REVERT: L 141 GLU cc_start: 0.6367 (tt0) cc_final: 0.6128 (tp30) outliers start: 69 outliers final: 29 residues processed: 345 average time/residue: 1.7593 time to fit residues: 692.6125 Evaluate side-chains 304 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 268 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 177 ARG Chi-restraints excluded: chain G residue 208 GLU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 281 optimal weight: 0.2980 chunk 230 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 339 optimal weight: 20.0000 chunk 366 optimal weight: 7.9990 chunk 302 optimal weight: 8.9990 chunk 336 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 272 optimal weight: 0.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 GLN D 170 GLN D 388 ASN D 448 GLN F 363 ASN F 425 GLN L 130 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30067 Z= 0.342 Angle : 0.588 6.938 40740 Z= 0.303 Chirality : 0.046 0.184 4567 Planarity : 0.005 0.049 5329 Dihedral : 6.163 155.695 4224 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.69 % Allowed : 12.49 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.66 (0.14), residues: 3761 helix: 1.34 (0.14), residues: 1525 sheet: -0.08 (0.22), residues: 563 loop : -0.12 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 100 HIS 0.005 0.001 HIS L 130 PHE 0.026 0.002 PHE A 269 TYR 0.015 0.002 TYR F 463 ARG 0.009 0.001 ARG E 345 *********************** 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 374 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 291 time to evaluate : 3.765 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8665 (tttt) REVERT: A 124 LYS cc_start: 0.7804 (mtmm) cc_final: 0.7432 (mttt) REVERT: A 130 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6672 (mtp-110) REVERT: A 133 MET cc_start: 0.7728 (mtt) cc_final: 0.7450 (mtm) REVERT: A 176 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6582 (mp0) REVERT: A 268 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7259 (mm-30) REVERT: A 456 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6670 (mp0) REVERT: A 491 ARG cc_start: 0.7376 (mtm-85) cc_final: 0.7058 (mtt-85) REVERT: B 45 ASP cc_start: 0.7338 (t0) cc_final: 0.6902 (t70) REVERT: B 48 PHE cc_start: 0.8304 (m-80) cc_final: 0.8089 (m-80) REVERT: B 62 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7203 (mt-10) REVERT: B 176 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6723 (mt-10) REVERT: B 207 THR cc_start: 0.8528 (m) cc_final: 0.8203 (p) REVERT: B 342 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: B 348 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7435 (mt-10) REVERT: B 500 TYR cc_start: 0.8140 (m-80) cc_final: 0.7907 (m-10) REVERT: B 524 LYS cc_start: 0.8543 (ttpp) cc_final: 0.7965 (mmtp) REVERT: B 527 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6660 (tt0) REVERT: B 538 GLU cc_start: 0.7079 (tt0) cc_final: 0.6029 (tp30) REVERT: B 540 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6732 (mm) REVERT: B 547 ARG cc_start: 0.7702 (mmm-85) cc_final: 0.6805 (tpp-160) REVERT: C 114 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7321 (mm-30) REVERT: C 470 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7022 (mt) REVERT: C 481 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7547 (mmm160) REVERT: C 525 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: C 547 ARG cc_start: 0.7464 (mmt-90) cc_final: 0.7114 (tpp-160) REVERT: D 77 GLU cc_start: 0.7579 (tt0) cc_final: 0.7274 (tt0) REVERT: D 128 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6779 (mp0) REVERT: D 465 GLN cc_start: 0.7574 (tt0) cc_final: 0.7347 (tm-30) REVERT: D 466 LYS cc_start: 0.7620 (tttp) cc_final: 0.6675 (mmtp) REVERT: E 6 LYS cc_start: 0.7814 (tttp) cc_final: 0.6950 (ptpt) REVERT: E 67 ASP cc_start: 0.8370 (p0) cc_final: 0.8013 (p0) REVERT: E 274 ARG cc_start: 0.7431 (mmm160) cc_final: 0.6690 (mtp180) REVERT: E 401 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6645 (mp0) REVERT: E 420 ARG cc_start: 0.7635 (mmm160) cc_final: 0.7266 (mmm-85) REVERT: E 428 GLN cc_start: 0.8569 (mt0) cc_final: 0.8271 (mt0) REVERT: F 6 LYS cc_start: 0.8187 (tttt) cc_final: 0.7378 (ptpt) REVERT: F 7 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7211 (mt-10) REVERT: F 61 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7638 (mm-30) REVERT: F 277 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8391 (mm) REVERT: F 380 ASP cc_start: 0.7675 (m-30) cc_final: 0.7379 (m-30) REVERT: F 409 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6761 (mtt90) REVERT: F 450 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7491 (mm-30) REVERT: G 9 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7344 (ptm) REVERT: G 105 LYS cc_start: 0.4499 (tptp) cc_final: 0.3538 (ptmm) REVERT: G 146 ARG cc_start: 0.7245 (mtp180) cc_final: 0.6841 (ttp-110) REVERT: G 149 LYS cc_start: 0.7675 (mmtt) cc_final: 0.7094 (mmmt) REVERT: G 153 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6861 (mm-30) REVERT: G 202 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6452 (tm-30) REVERT: H 8 GLU cc_start: 0.6222 (mp0) cc_final: 0.5483 (tm-30) REVERT: H 56 GLU cc_start: 0.6834 (pt0) cc_final: 0.5867 (pm20) REVERT: H 79 GLU cc_start: 0.6597 (tp30) cc_final: 0.6370 (tp30) REVERT: H 89 TYR cc_start: 0.7259 (t80) cc_final: 0.6990 (t80) REVERT: J 89 GLU cc_start: 0.6330 (mt-10) cc_final: 0.5888 (mp0) REVERT: J 110 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6149 (tp30) REVERT: J 113 GLU cc_start: 0.7181 (tt0) cc_final: 0.6773 (tt0) REVERT: J 122 VAL cc_start: 0.4328 (OUTLIER) cc_final: 0.4070 (p) REVERT: J 150 LEU cc_start: 0.5781 (OUTLIER) cc_final: 0.5294 (mp) REVERT: J 162 GLN cc_start: 0.7944 (mt0) cc_final: 0.7128 (mp10) REVERT: J 172 ASP cc_start: 0.6889 (m-30) cc_final: 0.6391 (t70) REVERT: K 100 ARG cc_start: 0.6015 (ttm110) cc_final: 0.5144 (mtt180) REVERT: L 81 GLU cc_start: 0.6822 (tp30) cc_final: 0.6318 (mm-30) REVERT: L 82 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.5796 (tm-30) REVERT: L 85 ARG cc_start: 0.6734 (ttp80) cc_final: 0.5575 (ttm170) REVERT: L 105 ARG cc_start: 0.6521 (mtm180) cc_final: 0.6307 (mtm-85) REVERT: L 138 ARG cc_start: 0.6674 (mmm160) cc_final: 0.6439 (mtt-85) REVERT: L 141 GLU cc_start: 0.6472 (tt0) cc_final: 0.6177 (tp30) outliers start: 83 outliers final: 29 residues processed: 351 average time/residue: 1.7769 time to fit residues: 711.9924 Evaluate side-chains 321 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 277 time to evaluate : 3.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 409 ARG Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 227 optimal weight: 0.6980 chunk 340 optimal weight: 1.9990 chunk 360 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 322 optimal weight: 0.0050 chunk 97 optimal weight: 8.9990 overall best weight: 2.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN C 316 GLN D 388 ASN D 448 GLN E 465 GLN F 425 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30067 Z= 0.206 Angle : 0.518 7.351 40740 Z= 0.265 Chirality : 0.043 0.191 4567 Planarity : 0.005 0.050 5329 Dihedral : 5.950 153.069 4224 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.95 % Allowed : 14.54 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.82 (0.14), residues: 3761 helix: 1.53 (0.14), residues: 1528 sheet: -0.06 (0.22), residues: 551 loop : -0.07 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 100 HIS 0.004 0.001 HIS L 130 PHE 0.016 0.001 PHE B 143 TYR 0.011 0.001 TYR F 463 ARG 0.009 0.000 ARG C 130 *********************** 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 347 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 287 time to evaluate : 3.416 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8648 (tttt) REVERT: A 93 ARG cc_start: 0.7653 (mmm-85) cc_final: 0.7306 (mmm160) REVERT: A 124 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7423 (mttt) REVERT: A 133 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7440 (mtm) REVERT: A 176 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6548 (mp0) REVERT: A 209 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7127 (mtm) REVERT: A 268 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7205 (mm-30) REVERT: A 456 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6716 (mp0) REVERT: A 491 ARG cc_start: 0.7312 (mtm-85) cc_final: 0.7019 (mtt-85) REVERT: A 524 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7192 (mptt) REVERT: B 45 ASP cc_start: 0.7266 (t0) cc_final: 0.6998 (t0) REVERT: B 48 PHE cc_start: 0.8266 (m-80) cc_final: 0.8036 (m-80) REVERT: B 62 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: B 207 THR cc_start: 0.8533 (m) cc_final: 0.8243 (p) REVERT: B 326 SER cc_start: 0.8329 (OUTLIER) cc_final: 0.8030 (p) REVERT: B 342 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: B 348 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7469 (mt-10) REVERT: B 500 TYR cc_start: 0.8115 (m-80) cc_final: 0.7902 (m-10) REVERT: B 524 LYS cc_start: 0.8537 (ttpp) cc_final: 0.7964 (mmtp) REVERT: B 538 GLU cc_start: 0.7055 (tt0) cc_final: 0.6073 (tp30) REVERT: B 540 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6721 (mm) REVERT: B 547 ARG cc_start: 0.7674 (mmm-85) cc_final: 0.6749 (tpp-160) REVERT: C 470 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6987 (mt) REVERT: C 481 ARG cc_start: 0.7954 (mtp180) cc_final: 0.7549 (mmm160) REVERT: D 77 GLU cc_start: 0.7595 (tt0) cc_final: 0.7293 (tt0) REVERT: D 128 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6743 (mp0) REVERT: D 465 GLN cc_start: 0.7526 (tt0) cc_final: 0.7311 (tm-30) REVERT: D 466 LYS cc_start: 0.7680 (tttp) cc_final: 0.6792 (mmtp) REVERT: E 6 LYS cc_start: 0.7810 (tttp) cc_final: 0.6954 (ptpt) REVERT: E 67 ASP cc_start: 0.8407 (p0) cc_final: 0.8066 (p0) REVERT: E 274 ARG cc_start: 0.7413 (mmm160) cc_final: 0.6649 (mtp180) REVERT: E 401 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6595 (mp0) REVERT: E 420 ARG cc_start: 0.7656 (mmm160) cc_final: 0.7285 (mmm-85) REVERT: E 428 GLN cc_start: 0.8583 (mt0) cc_final: 0.8282 (mt0) REVERT: F 6 LYS cc_start: 0.8180 (tttt) cc_final: 0.7369 (ptpt) REVERT: F 7 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7202 (mt-10) REVERT: F 277 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8366 (mm) REVERT: F 380 ASP cc_start: 0.7686 (m-30) cc_final: 0.7370 (m-30) REVERT: F 409 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6611 (mtt90) REVERT: F 450 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7416 (mm-30) REVERT: G 105 LYS cc_start: 0.4348 (tptp) cc_final: 0.3435 (ptmm) REVERT: G 146 ARG cc_start: 0.7193 (mtp180) cc_final: 0.6797 (ttp-110) REVERT: G 149 LYS cc_start: 0.7637 (mmtt) cc_final: 0.7023 (mmmt) REVERT: G 153 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6914 (mm-30) REVERT: G 202 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6372 (tm-30) REVERT: H 67 ASP cc_start: 0.4983 (OUTLIER) cc_final: 0.4492 (m-30) REVERT: H 79 GLU cc_start: 0.6606 (tp30) cc_final: 0.6395 (tp30) REVERT: J 110 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6153 (tp30) REVERT: J 113 GLU cc_start: 0.7222 (tt0) cc_final: 0.6911 (tt0) REVERT: J 122 VAL cc_start: 0.4219 (OUTLIER) cc_final: 0.3984 (p) REVERT: J 150 LEU cc_start: 0.5710 (OUTLIER) cc_final: 0.5220 (mp) REVERT: J 162 GLN cc_start: 0.7991 (mt0) cc_final: 0.7326 (mt0) REVERT: K 100 ARG cc_start: 0.5960 (ttm110) cc_final: 0.5127 (mtt180) REVERT: L 81 GLU cc_start: 0.6850 (tp30) cc_final: 0.6214 (mm-30) REVERT: L 82 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6227 (tp30) REVERT: L 85 ARG cc_start: 0.6791 (ttp80) cc_final: 0.5628 (ttm170) REVERT: L 105 ARG cc_start: 0.6536 (mtm180) cc_final: 0.6314 (mtm-85) REVERT: L 138 ARG cc_start: 0.6675 (mmm160) cc_final: 0.6414 (mtt-85) REVERT: L 141 GLU cc_start: 0.6431 (tt0) cc_final: 0.6186 (tp30) outliers start: 60 outliers final: 29 residues processed: 330 average time/residue: 1.7929 time to fit residues: 675.5138 Evaluate side-chains 318 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 274 time to evaluate : 3.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 409 ARG Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 0.0170 chunk 204 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 268 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 307 optimal weight: 6.9990 chunk 249 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 323 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 overall best weight: 4.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN C 316 GLN C 459 GLN D 388 ASN D 448 GLN F 425 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 30067 Z= 0.393 Angle : 0.609 6.980 40740 Z= 0.312 Chirality : 0.047 0.197 4567 Planarity : 0.005 0.051 5329 Dihedral : 6.176 147.396 4224 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.76 % Allowed : 15.28 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 1.21 (0.14), residues: 1532 sheet: -0.12 (0.22), residues: 549 loop : -0.26 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 100 HIS 0.004 0.001 HIS L 130 PHE 0.019 0.002 PHE A 269 TYR 0.014 0.002 TYR F 463 ARG 0.010 0.001 ARG E 345 *********************** 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 361 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 276 time to evaluate : 3.325 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8670 (tttt) REVERT: A 124 LYS cc_start: 0.7820 (mtmm) cc_final: 0.7435 (mttt) REVERT: A 130 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6709 (mtp-110) REVERT: A 133 MET cc_start: 0.7671 (mtt) cc_final: 0.7398 (mtm) REVERT: A 268 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7185 (mm-30) REVERT: A 456 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6681 (mp0) REVERT: A 491 ARG cc_start: 0.7391 (mtm-85) cc_final: 0.6997 (mtt-85) REVERT: A 524 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7233 (mptt) REVERT: B 45 ASP cc_start: 0.7301 (t0) cc_final: 0.6936 (t0) REVERT: B 48 PHE cc_start: 0.8337 (m-80) cc_final: 0.8121 (m-80) REVERT: B 62 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7244 (mt-10) REVERT: B 207 THR cc_start: 0.8580 (m) cc_final: 0.8263 (p) REVERT: B 342 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: B 348 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7454 (mt-10) REVERT: B 500 TYR cc_start: 0.8104 (m-80) cc_final: 0.7900 (m-10) REVERT: B 524 LYS cc_start: 0.8564 (ttpp) cc_final: 0.7979 (mmtp) REVERT: B 527 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6630 (tt0) REVERT: B 538 GLU cc_start: 0.7083 (tt0) cc_final: 0.6079 (tp30) REVERT: B 540 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6712 (mm) REVERT: B 547 ARG cc_start: 0.7634 (mmm-85) cc_final: 0.6742 (tpp-160) REVERT: C 470 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7060 (mt) REVERT: D 77 GLU cc_start: 0.7609 (tt0) cc_final: 0.7322 (tt0) REVERT: D 128 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6896 (mp0) REVERT: D 373 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7152 (pt0) REVERT: D 466 LYS cc_start: 0.7748 (tttp) cc_final: 0.6688 (mmtp) REVERT: E 6 LYS cc_start: 0.7847 (tttp) cc_final: 0.7009 (ptpt) REVERT: E 274 ARG cc_start: 0.7476 (mmm160) cc_final: 0.6705 (mtp180) REVERT: E 391 ASP cc_start: 0.7667 (p0) cc_final: 0.7431 (p0) REVERT: E 401 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6646 (mp0) REVERT: E 420 ARG cc_start: 0.7670 (mmm160) cc_final: 0.7294 (mmm-85) REVERT: E 428 GLN cc_start: 0.8540 (mt0) cc_final: 0.8256 (mt0) REVERT: F 6 LYS cc_start: 0.8326 (tttt) cc_final: 0.7374 (ptpt) REVERT: F 7 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7275 (mt-10) REVERT: F 36 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8366 (ttmt) REVERT: F 61 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7682 (mm-30) REVERT: F 334 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: F 380 ASP cc_start: 0.7702 (m-30) cc_final: 0.7395 (m-30) REVERT: F 409 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6823 (mtt90) REVERT: F 450 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7487 (mm-30) REVERT: G 105 LYS cc_start: 0.4536 (tptp) cc_final: 0.3629 (ptmt) REVERT: G 146 ARG cc_start: 0.7239 (mtp180) cc_final: 0.6911 (ttp-110) REVERT: G 149 LYS cc_start: 0.7711 (mmtt) cc_final: 0.7096 (mmmt) REVERT: G 153 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6931 (mm-30) REVERT: G 202 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6423 (tm-30) REVERT: H 67 ASP cc_start: 0.5047 (OUTLIER) cc_final: 0.4467 (m-30) REVERT: J 89 GLU cc_start: 0.6362 (mt-10) cc_final: 0.5890 (mp0) REVERT: J 110 GLU cc_start: 0.6647 (mt-10) cc_final: 0.6136 (tp30) REVERT: J 113 GLU cc_start: 0.7238 (tt0) cc_final: 0.6975 (tt0) REVERT: J 122 VAL cc_start: 0.4052 (OUTLIER) cc_final: 0.3786 (p) REVERT: J 150 LEU cc_start: 0.5757 (OUTLIER) cc_final: 0.5148 (mp) REVERT: J 162 GLN cc_start: 0.7979 (mt0) cc_final: 0.7309 (mt0) REVERT: K 100 ARG cc_start: 0.5953 (ttm110) cc_final: 0.5157 (mtt180) REVERT: K 101 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6760 (mm-30) REVERT: L 81 GLU cc_start: 0.6854 (tp30) cc_final: 0.6232 (mm-30) REVERT: L 82 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.5802 (tm-30) REVERT: L 85 ARG cc_start: 0.6765 (ttp80) cc_final: 0.5565 (ttm170) REVERT: L 105 ARG cc_start: 0.6590 (mtm180) cc_final: 0.6371 (mtm-85) REVERT: L 138 ARG cc_start: 0.6691 (mmm160) cc_final: 0.6231 (mmm160) REVERT: L 141 GLU cc_start: 0.6487 (tt0) cc_final: 0.6223 (tp30) outliers start: 85 outliers final: 38 residues processed: 341 average time/residue: 1.7099 time to fit residues: 667.8591 Evaluate side-chains 323 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 268 time to evaluate : 3.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 409 ARG Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 177 ARG Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 4.9990 chunk 324 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 360 optimal weight: 8.9990 chunk 299 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN D 388 ASN D 448 GLN F 425 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30067 Z= 0.188 Angle : 0.505 7.450 40740 Z= 0.257 Chirality : 0.042 0.207 4567 Planarity : 0.004 0.050 5329 Dihedral : 5.839 142.188 4224 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.98 % Allowed : 16.26 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 1.53 (0.14), residues: 1550 sheet: -0.07 (0.22), residues: 553 loop : -0.13 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 100 HIS 0.004 0.001 HIS L 130 PHE 0.014 0.001 PHE A 230 TYR 0.011 0.001 TYR G 133 ARG 0.010 0.000 ARG C 130 *********************** 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 345 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 284 time to evaluate : 3.507 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8639 (tttt) REVERT: A 93 ARG cc_start: 0.7632 (mmm-85) cc_final: 0.7195 (mmm160) REVERT: A 124 LYS cc_start: 0.7843 (mtmm) cc_final: 0.7455 (mttt) REVERT: A 268 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7191 (mm-30) REVERT: A 456 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6741 (mp0) REVERT: A 491 ARG cc_start: 0.7250 (mtm-85) cc_final: 0.6874 (mtt-85) REVERT: A 524 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.7168 (mptt) REVERT: B 45 ASP cc_start: 0.7188 (t0) cc_final: 0.6906 (t0) REVERT: B 62 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7202 (mt-10) REVERT: B 207 THR cc_start: 0.8528 (m) cc_final: 0.8231 (p) REVERT: B 269 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8155 (t80) REVERT: B 326 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.8023 (p) REVERT: B 364 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8369 (mtt180) REVERT: B 524 LYS cc_start: 0.8548 (ttpp) cc_final: 0.7939 (mmtp) REVERT: B 538 GLU cc_start: 0.7076 (tt0) cc_final: 0.6027 (tp30) REVERT: B 540 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6739 (mm) REVERT: B 547 ARG cc_start: 0.7583 (mmm-85) cc_final: 0.6734 (tpp-160) REVERT: C 470 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6977 (mt) REVERT: D 77 GLU cc_start: 0.7569 (tt0) cc_final: 0.7306 (tt0) REVERT: D 128 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6809 (mp0) REVERT: D 466 LYS cc_start: 0.7714 (tttp) cc_final: 0.6900 (mmtp) REVERT: E 6 LYS cc_start: 0.7801 (tttp) cc_final: 0.6954 (ptpt) REVERT: E 67 ASP cc_start: 0.8486 (p0) cc_final: 0.8136 (p0) REVERT: E 274 ARG cc_start: 0.7421 (mmm160) cc_final: 0.6657 (mtp180) REVERT: E 302 GLU cc_start: 0.7872 (pp20) cc_final: 0.7636 (pt0) REVERT: E 391 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7405 (p0) REVERT: E 401 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6659 (mp0) REVERT: E 420 ARG cc_start: 0.7603 (mmm160) cc_final: 0.7231 (mmm-85) REVERT: E 428 GLN cc_start: 0.8575 (mt0) cc_final: 0.8284 (mt0) REVERT: F 6 LYS cc_start: 0.8282 (tttt) cc_final: 0.7301 (ptpt) REVERT: F 7 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7209 (mt-10) REVERT: F 36 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8357 (ttmt) REVERT: F 380 ASP cc_start: 0.7692 (m-30) cc_final: 0.7374 (m-30) REVERT: F 409 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6705 (mtt90) REVERT: F 450 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7360 (mm-30) REVERT: G 105 LYS cc_start: 0.4512 (tptp) cc_final: 0.3558 (ptmm) REVERT: G 146 ARG cc_start: 0.7160 (mtp180) cc_final: 0.6817 (ttp-110) REVERT: G 149 LYS cc_start: 0.7674 (mmtt) cc_final: 0.7139 (tptp) REVERT: G 153 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6952 (mm-30) REVERT: G 202 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6327 (tm-30) REVERT: H 67 ASP cc_start: 0.5007 (OUTLIER) cc_final: 0.4493 (m-30) REVERT: H 79 GLU cc_start: 0.6477 (tp30) cc_final: 0.5816 (tm-30) REVERT: J 110 GLU cc_start: 0.6611 (mt-10) cc_final: 0.6138 (tp30) REVERT: J 113 GLU cc_start: 0.7144 (tt0) cc_final: 0.6921 (tt0) REVERT: J 150 LEU cc_start: 0.5339 (OUTLIER) cc_final: 0.4864 (mp) REVERT: J 162 GLN cc_start: 0.8034 (mt0) cc_final: 0.7270 (mp10) REVERT: K 100 ARG cc_start: 0.5988 (ttm110) cc_final: 0.5213 (mtt180) REVERT: L 74 GLN cc_start: 0.6990 (mm-40) cc_final: 0.6535 (mm110) REVERT: L 81 GLU cc_start: 0.6839 (tp30) cc_final: 0.6226 (mm-30) REVERT: L 82 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.5835 (tm-30) REVERT: L 85 ARG cc_start: 0.6753 (ttp80) cc_final: 0.5573 (ttm170) REVERT: L 105 ARG cc_start: 0.6518 (mtm180) cc_final: 0.6293 (mtm-85) REVERT: L 138 ARG cc_start: 0.6831 (mmm160) cc_final: 0.6321 (mmm160) REVERT: L 141 GLU cc_start: 0.6448 (tt0) cc_final: 0.6245 (tp30) outliers start: 61 outliers final: 30 residues processed: 331 average time/residue: 1.7351 time to fit residues: 660.9772 Evaluate side-chains 310 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 266 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 391 ASP Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 409 ARG Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 263 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 303 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 359 optimal weight: 20.0000 chunk 224 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN D 388 ASN D 448 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30067 Z= 0.279 Angle : 0.555 7.384 40740 Z= 0.283 Chirality : 0.044 0.218 4567 Planarity : 0.005 0.050 5329 Dihedral : 5.923 136.585 4223 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.73 % Allowed : 16.16 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.70 (0.14), residues: 3761 helix: 1.45 (0.14), residues: 1540 sheet: -0.11 (0.22), residues: 562 loop : -0.18 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 100 HIS 0.004 0.001 HIS F 252 PHE 0.016 0.002 PHE B 143 TYR 0.013 0.001 TYR F 463 ARG 0.012 0.000 ARG C 130 *********************** 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 360 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 276 time to evaluate : 3.330 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8665 (tttt) REVERT: A 93 ARG cc_start: 0.7633 (mmm-85) cc_final: 0.7182 (mmm160) REVERT: A 124 LYS cc_start: 0.7810 (mtmm) cc_final: 0.7367 (mttt) REVERT: A 268 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7204 (mm-30) REVERT: A 456 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6679 (mp0) REVERT: A 491 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.7004 (mtt-85) REVERT: A 524 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7223 (mptt) REVERT: B 45 ASP cc_start: 0.7237 (t0) cc_final: 0.6874 (t0) REVERT: B 62 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7229 (mt-10) REVERT: B 207 THR cc_start: 0.8541 (m) cc_final: 0.8250 (p) REVERT: B 269 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8147 (t80) REVERT: B 364 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8365 (mtt180) REVERT: B 524 LYS cc_start: 0.8557 (ttpp) cc_final: 0.7940 (mmtp) REVERT: B 538 GLU cc_start: 0.7087 (tt0) cc_final: 0.6073 (tp30) REVERT: B 540 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6659 (mm) REVERT: B 547 ARG cc_start: 0.7626 (mmm-85) cc_final: 0.6846 (tpp-160) REVERT: C 470 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7054 (mt) REVERT: D 77 GLU cc_start: 0.7609 (tt0) cc_final: 0.7341 (tt0) REVERT: D 128 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6829 (mp0) REVERT: D 302 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: D 465 GLN cc_start: 0.7497 (tt0) cc_final: 0.7221 (tm-30) REVERT: D 466 LYS cc_start: 0.7838 (tttp) cc_final: 0.6790 (mmtp) REVERT: E 6 LYS cc_start: 0.7837 (tttp) cc_final: 0.6998 (ptpt) REVERT: E 274 ARG cc_start: 0.7459 (mmm160) cc_final: 0.6713 (mtp180) REVERT: E 391 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7396 (p0) REVERT: E 401 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6653 (mp0) REVERT: E 420 ARG cc_start: 0.7626 (mmm160) cc_final: 0.7243 (mmm-85) REVERT: E 428 GLN cc_start: 0.8571 (mt0) cc_final: 0.8283 (mt0) REVERT: F 6 LYS cc_start: 0.8282 (tttt) cc_final: 0.7313 (ptpt) REVERT: F 7 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7213 (mt-10) REVERT: F 36 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8356 (ttmt) REVERT: F 380 ASP cc_start: 0.7713 (m-30) cc_final: 0.7383 (m-30) REVERT: F 409 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6740 (mtt90) REVERT: F 450 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7492 (mm-30) REVERT: G 105 LYS cc_start: 0.4596 (tptp) cc_final: 0.3734 (pttp) REVERT: G 146 ARG cc_start: 0.7221 (mtp180) cc_final: 0.6902 (ttp-110) REVERT: G 149 LYS cc_start: 0.7675 (mmtt) cc_final: 0.7220 (mmmt) REVERT: G 153 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6876 (mm-30) REVERT: G 202 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6389 (tm-30) REVERT: H 67 ASP cc_start: 0.5110 (OUTLIER) cc_final: 0.4559 (m-30) REVERT: H 78 LYS cc_start: 0.6870 (mmpt) cc_final: 0.6553 (mttp) REVERT: H 79 GLU cc_start: 0.6419 (tp30) cc_final: 0.5686 (tm-30) REVERT: H 87 GLU cc_start: 0.6577 (mm-30) cc_final: 0.5468 (pm20) REVERT: J 89 GLU cc_start: 0.6367 (mt-10) cc_final: 0.5907 (mp0) REVERT: J 110 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6187 (tp30) REVERT: J 113 GLU cc_start: 0.7165 (tt0) cc_final: 0.6944 (tt0) REVERT: J 122 VAL cc_start: 0.3913 (OUTLIER) cc_final: 0.3683 (p) REVERT: J 150 LEU cc_start: 0.5388 (OUTLIER) cc_final: 0.4908 (mp) REVERT: J 162 GLN cc_start: 0.8002 (mt0) cc_final: 0.7230 (mp10) REVERT: K 100 ARG cc_start: 0.5993 (ttm110) cc_final: 0.5161 (mtt180) REVERT: L 81 GLU cc_start: 0.6832 (tp30) cc_final: 0.6216 (mm-30) REVERT: L 82 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.5772 (tm-30) REVERT: L 85 ARG cc_start: 0.6722 (ttp80) cc_final: 0.5519 (ttm170) REVERT: L 105 ARG cc_start: 0.6475 (mtm180) cc_final: 0.6256 (mtm-85) REVERT: L 138 ARG cc_start: 0.6740 (mmm160) cc_final: 0.6234 (mmm160) REVERT: L 141 GLU cc_start: 0.6477 (tt0) cc_final: 0.6208 (tp30) outliers start: 84 outliers final: 44 residues processed: 341 average time/residue: 1.6611 time to fit residues: 650.1899 Evaluate side-chains 330 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 271 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 391 ASP Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 409 ARG Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 69 optimal weight: 0.0030 chunk 228 optimal weight: 0.0980 chunk 244 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 282 optimal weight: 7.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN D 388 ASN D 407 ASN D 448 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30067 Z= 0.149 Angle : 0.485 8.805 40740 Z= 0.245 Chirality : 0.041 0.225 4567 Planarity : 0.004 0.048 5329 Dihedral : 5.579 130.573 4223 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.59 % Allowed : 17.55 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 1.01 (0.14), residues: 3761 helix: 1.76 (0.14), residues: 1541 sheet: -0.02 (0.22), residues: 560 loop : -0.03 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 100 HIS 0.004 0.001 HIS C 418 PHE 0.011 0.001 PHE C 230 TYR 0.011 0.001 TYR G 61 ARG 0.012 0.000 ARG C 130 *********************** 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 340 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 291 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8639 (tttt) REVERT: A 93 ARG cc_start: 0.7548 (mmm-85) cc_final: 0.7253 (mmm160) REVERT: A 124 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7415 (mttt) REVERT: A 268 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7197 (mm-30) REVERT: A 456 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6731 (mp0) REVERT: A 491 ARG cc_start: 0.7303 (mtm-85) cc_final: 0.6818 (mtt-85) REVERT: A 524 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7200 (mptt) REVERT: B 45 ASP cc_start: 0.7156 (t0) cc_final: 0.6899 (t70) REVERT: B 62 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7474 (mt-10) REVERT: B 207 THR cc_start: 0.8473 (m) cc_final: 0.8228 (p) REVERT: B 269 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8108 (t80) REVERT: B 326 SER cc_start: 0.8197 (OUTLIER) cc_final: 0.7960 (p) REVERT: B 425 ASN cc_start: 0.7820 (m110) cc_final: 0.7365 (m-40) REVERT: B 524 LYS cc_start: 0.8564 (ttpp) cc_final: 0.7925 (mmtp) REVERT: B 538 GLU cc_start: 0.6959 (tt0) cc_final: 0.6151 (mm-30) REVERT: B 540 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6743 (mm) REVERT: B 547 ARG cc_start: 0.7613 (mmm-85) cc_final: 0.7154 (tpp-160) REVERT: C 470 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6898 (mt) REVERT: C 491 ARG cc_start: 0.7611 (ptt-90) cc_final: 0.7409 (ptp90) REVERT: C 538 GLU cc_start: 0.7748 (mp0) cc_final: 0.7491 (pm20) REVERT: D 77 GLU cc_start: 0.7546 (tt0) cc_final: 0.7282 (tt0) REVERT: D 128 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6781 (mp0) REVERT: D 302 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7116 (tt0) REVERT: D 465 GLN cc_start: 0.7504 (tt0) cc_final: 0.7228 (tm-30) REVERT: D 466 LYS cc_start: 0.7883 (tttp) cc_final: 0.6911 (mmtp) REVERT: E 6 LYS cc_start: 0.7732 (tttp) cc_final: 0.6898 (ptpt) REVERT: E 67 ASP cc_start: 0.8475 (p0) cc_final: 0.8121 (p0) REVERT: E 274 ARG cc_start: 0.7413 (mmm160) cc_final: 0.6616 (mtp180) REVERT: E 401 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6619 (mp0) REVERT: E 420 ARG cc_start: 0.7560 (mmm160) cc_final: 0.7130 (mmm-85) REVERT: E 428 GLN cc_start: 0.8602 (mt0) cc_final: 0.8310 (mt0) REVERT: F 6 LYS cc_start: 0.8249 (tttt) cc_final: 0.7318 (ptpt) REVERT: F 7 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7143 (mt-10) REVERT: F 36 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8349 (ttmt) REVERT: F 380 ASP cc_start: 0.7610 (m-30) cc_final: 0.7269 (m-30) REVERT: F 450 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7364 (mm-30) REVERT: G 105 LYS cc_start: 0.4543 (tptp) cc_final: 0.3711 (pttp) REVERT: G 146 ARG cc_start: 0.7152 (mtp180) cc_final: 0.6788 (ttp-110) REVERT: G 149 LYS cc_start: 0.7677 (mmtt) cc_final: 0.7240 (mmmt) REVERT: G 153 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6846 (mm-30) REVERT: G 202 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6324 (tm-30) REVERT: I 93 GLU cc_start: 0.6293 (mm-30) cc_final: 0.5923 (mp0) REVERT: J 89 GLU cc_start: 0.6307 (mt-10) cc_final: 0.5867 (mp0) REVERT: J 110 GLU cc_start: 0.6588 (mt-10) cc_final: 0.6125 (tp30) REVERT: J 150 LEU cc_start: 0.5237 (OUTLIER) cc_final: 0.4765 (mp) REVERT: J 162 GLN cc_start: 0.7967 (mt0) cc_final: 0.7260 (mp10) REVERT: K 100 ARG cc_start: 0.6004 (ttm110) cc_final: 0.5222 (mtt180) REVERT: L 74 GLN cc_start: 0.7035 (mm-40) cc_final: 0.6583 (mm110) REVERT: L 81 GLU cc_start: 0.6868 (tp30) cc_final: 0.6233 (mm-30) REVERT: L 82 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6323 (tp30) REVERT: L 85 ARG cc_start: 0.6795 (ttp80) cc_final: 0.5635 (ttm170) REVERT: L 105 ARG cc_start: 0.6413 (mtm180) cc_final: 0.6186 (mtm-85) REVERT: L 138 ARG cc_start: 0.6818 (mmm160) cc_final: 0.6312 (mmm160) REVERT: L 161 THR cc_start: 0.8011 (p) cc_final: 0.7753 (t) outliers start: 49 outliers final: 25 residues processed: 328 average time/residue: 1.7053 time to fit residues: 643.4706 Evaluate side-chains 303 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 267 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 7.9990 chunk 344 optimal weight: 8.9990 chunk 314 optimal weight: 2.9990 chunk 335 optimal weight: 2.9990 chunk 201 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 263 optimal weight: 0.3980 chunk 102 optimal weight: 9.9990 chunk 302 optimal weight: 6.9990 chunk 316 optimal weight: 8.9990 chunk 333 optimal weight: 9.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN C 541 GLN D 377 GLN D 388 ASN D 407 ASN D 448 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30067 Z= 0.323 Angle : 0.576 11.875 40740 Z= 0.294 Chirality : 0.045 0.226 4567 Planarity : 0.005 0.064 5329 Dihedral : 5.846 131.719 4223 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.95 % Allowed : 17.59 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.75 (0.14), residues: 3761 helix: 1.49 (0.14), residues: 1543 sheet: -0.09 (0.22), residues: 555 loop : -0.15 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 100 HIS 0.004 0.001 HIS D 249 PHE 0.017 0.002 PHE C 559 TYR 0.013 0.001 TYR F 463 ARG 0.017 0.000 ARG E 345 *********************** 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 326 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 266 time to evaluate : 3.347 Fit side-chains REVERT: A 8 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8678 (tttt) REVERT: A 93 ARG cc_start: 0.7600 (mmm-85) cc_final: 0.7177 (mmm160) REVERT: A 124 LYS cc_start: 0.7864 (mtmm) cc_final: 0.7414 (mttt) REVERT: A 268 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7217 (mm-30) REVERT: A 456 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6683 (mp0) REVERT: A 491 ARG cc_start: 0.7358 (mtm-85) cc_final: 0.6845 (mtt-85) REVERT: A 524 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7240 (mptt) REVERT: B 45 ASP cc_start: 0.7237 (t0) cc_final: 0.6876 (t0) REVERT: B 62 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7229 (mt-10) REVERT: B 158 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7375 (ttmm) REVERT: B 207 THR cc_start: 0.8550 (m) cc_final: 0.8253 (p) REVERT: B 220 MET cc_start: 0.8306 (tpt) cc_final: 0.7953 (tpt) REVERT: B 269 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8141 (t80) REVERT: B 364 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8400 (mtt180) REVERT: B 524 LYS cc_start: 0.8567 (ttpp) cc_final: 0.7933 (mmtp) REVERT: B 538 GLU cc_start: 0.7046 (tt0) cc_final: 0.6205 (mm-30) REVERT: B 540 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6721 (mm) REVERT: B 547 ARG cc_start: 0.7626 (mmm-85) cc_final: 0.6860 (tpp-160) REVERT: C 124 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7987 (tppt) REVERT: C 470 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7005 (mt) REVERT: D 77 GLU cc_start: 0.7570 (tt0) cc_final: 0.7282 (mt-10) REVERT: D 128 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6842 (mp0) REVERT: D 302 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: D 466 LYS cc_start: 0.7902 (tttp) cc_final: 0.6880 (mmtp) REVERT: E 6 LYS cc_start: 0.7780 (tttp) cc_final: 0.6977 (ptpt) REVERT: E 274 ARG cc_start: 0.7491 (mmm160) cc_final: 0.6715 (mtp180) REVERT: E 302 GLU cc_start: 0.7938 (pp20) cc_final: 0.7608 (pt0) REVERT: E 401 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6659 (mp0) REVERT: E 420 ARG cc_start: 0.7618 (mmm160) cc_final: 0.7214 (mmm-85) REVERT: E 428 GLN cc_start: 0.8575 (mt0) cc_final: 0.8312 (mt0) REVERT: F 6 LYS cc_start: 0.8333 (tttt) cc_final: 0.7304 (ptpt) REVERT: F 7 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7213 (mt-10) REVERT: F 36 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8360 (ttmt) REVERT: F 380 ASP cc_start: 0.7719 (m-30) cc_final: 0.7394 (m-30) REVERT: F 450 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7544 (mm-30) REVERT: G 105 LYS cc_start: 0.4491 (tptp) cc_final: 0.3660 (pttp) REVERT: G 146 ARG cc_start: 0.7265 (mtp180) cc_final: 0.6918 (ttp-110) REVERT: G 149 LYS cc_start: 0.7675 (mmtt) cc_final: 0.7234 (mmmt) REVERT: G 153 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6921 (mm-30) REVERT: G 202 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6359 (tm-30) REVERT: H 79 GLU cc_start: 0.6352 (tp30) cc_final: 0.5475 (tm-30) REVERT: H 87 GLU cc_start: 0.6446 (mm-30) cc_final: 0.5239 (pm20) REVERT: I 93 GLU cc_start: 0.6136 (mm-30) cc_final: 0.5735 (mp0) REVERT: J 89 GLU cc_start: 0.6372 (mt-10) cc_final: 0.5907 (mp0) REVERT: J 110 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6166 (tp30) REVERT: J 150 LEU cc_start: 0.5383 (OUTLIER) cc_final: 0.4898 (mp) REVERT: J 162 GLN cc_start: 0.7983 (mt0) cc_final: 0.7231 (mp10) REVERT: K 100 ARG cc_start: 0.6037 (ttm110) cc_final: 0.5260 (mtt180) REVERT: L 74 GLN cc_start: 0.7009 (mm-40) cc_final: 0.6457 (mm110) REVERT: L 81 GLU cc_start: 0.6816 (tp30) cc_final: 0.6268 (mm-30) REVERT: L 82 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.5769 (tm-30) REVERT: L 85 ARG cc_start: 0.6720 (ttp80) cc_final: 0.5555 (ttm170) REVERT: L 105 ARG cc_start: 0.6475 (mtm180) cc_final: 0.6250 (mtm-85) REVERT: L 138 ARG cc_start: 0.6835 (mmm160) cc_final: 0.6286 (mmm160) outliers start: 60 outliers final: 35 residues processed: 316 average time/residue: 1.7007 time to fit residues: 615.7800 Evaluate side-chains 310 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 262 time to evaluate : 3.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 3.9990 chunk 354 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 371 optimal weight: 9.9990 chunk 342 optimal weight: 20.0000 chunk 295 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 181 optimal weight: 0.0470 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 388 ASN D 448 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30067 Z= 0.253 Angle : 0.541 7.652 40740 Z= 0.277 Chirality : 0.044 0.242 4567 Planarity : 0.005 0.057 5329 Dihedral : 5.796 131.467 4223 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.85 % Allowed : 17.78 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.74 (0.14), residues: 3761 helix: 1.51 (0.14), residues: 1542 sheet: -0.14 (0.22), residues: 558 loop : -0.16 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 471 HIS 0.006 0.001 HIS B 418 PHE 0.015 0.002 PHE A 230 TYR 0.012 0.001 TYR F 463 ARG 0.014 0.000 ARG E 345 ********************** 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 318 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 261 time to evaluate : 3.136 Fit side-chains REVERT: A 8 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8646 (tttt) REVERT: A 93 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.7161 (mmm160) REVERT: A 124 LYS cc_start: 0.7838 (mtmm) cc_final: 0.7408 (mttt) REVERT: A 268 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7214 (mm-30) REVERT: A 456 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6704 (mp0) REVERT: A 491 ARG cc_start: 0.7377 (mtm-85) cc_final: 0.6864 (mtt-85) REVERT: A 524 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7195 (mptt) REVERT: B 45 ASP cc_start: 0.7202 (t0) cc_final: 0.6878 (t0) REVERT: B 62 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: B 158 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7413 (ttmm) REVERT: B 207 THR cc_start: 0.8537 (m) cc_final: 0.8246 (p) REVERT: B 269 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8129 (t80) REVERT: B 326 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.7918 (p) REVERT: B 364 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8408 (mtt180) REVERT: B 417 ARG cc_start: 0.7425 (mmm160) cc_final: 0.7072 (mmm-85) REVERT: B 425 ASN cc_start: 0.7910 (m110) cc_final: 0.7454 (m-40) REVERT: B 524 LYS cc_start: 0.8570 (ttpp) cc_final: 0.7931 (mmtp) REVERT: B 538 GLU cc_start: 0.7026 (tt0) cc_final: 0.6194 (mm-30) REVERT: B 540 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6735 (mm) REVERT: B 547 ARG cc_start: 0.7609 (mmm-85) cc_final: 0.6812 (tpp-160) REVERT: C 124 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8016 (tppt) REVERT: C 470 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6974 (mt) REVERT: D 77 GLU cc_start: 0.7554 (tt0) cc_final: 0.7303 (tt0) REVERT: D 115 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7701 (p) REVERT: D 128 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6832 (mp0) REVERT: D 302 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: D 466 LYS cc_start: 0.7840 (tttp) cc_final: 0.6885 (mmtp) REVERT: E 6 LYS cc_start: 0.7775 (tttp) cc_final: 0.6967 (ptpt) REVERT: E 274 ARG cc_start: 0.7488 (mmm160) cc_final: 0.6695 (mtp180) REVERT: E 401 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6677 (mp0) REVERT: E 420 ARG cc_start: 0.7640 (mmm160) cc_final: 0.7216 (mmm-85) REVERT: E 428 GLN cc_start: 0.8582 (mt0) cc_final: 0.8312 (mt0) REVERT: F 6 LYS cc_start: 0.8329 (tttt) cc_final: 0.7295 (ptpt) REVERT: F 7 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7166 (mt-10) REVERT: F 36 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8329 (ttmt) REVERT: F 380 ASP cc_start: 0.7689 (m-30) cc_final: 0.7356 (m-30) REVERT: F 409 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6735 (mtt90) REVERT: F 450 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7501 (mm-30) REVERT: G 105 LYS cc_start: 0.4600 (tptp) cc_final: 0.3732 (pttp) REVERT: G 146 ARG cc_start: 0.7251 (mtp180) cc_final: 0.6873 (ttp-170) REVERT: G 149 LYS cc_start: 0.7671 (mmtt) cc_final: 0.7231 (mmmt) REVERT: G 153 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6915 (mm-30) REVERT: G 181 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7142 (mt0) REVERT: G 202 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6354 (tm-30) REVERT: H 79 GLU cc_start: 0.6329 (tp30) cc_final: 0.5442 (tm-30) REVERT: H 87 GLU cc_start: 0.6360 (mm-30) cc_final: 0.5200 (pm20) REVERT: I 93 GLU cc_start: 0.6152 (mm-30) cc_final: 0.5760 (mp0) REVERT: J 89 GLU cc_start: 0.6375 (mt-10) cc_final: 0.5908 (mp0) REVERT: J 110 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6096 (tp30) REVERT: J 150 LEU cc_start: 0.5345 (OUTLIER) cc_final: 0.4870 (mp) REVERT: J 162 GLN cc_start: 0.7970 (mt0) cc_final: 0.7230 (mp10) REVERT: K 100 ARG cc_start: 0.6027 (ttm110) cc_final: 0.5241 (mtt180) REVERT: L 74 GLN cc_start: 0.6997 (mm-40) cc_final: 0.6472 (mm110) REVERT: L 81 GLU cc_start: 0.6800 (tp30) cc_final: 0.6248 (mm-30) REVERT: L 82 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.5737 (tm-30) REVERT: L 85 ARG cc_start: 0.6737 (ttp80) cc_final: 0.5564 (ttm170) REVERT: L 105 ARG cc_start: 0.6455 (mtm180) cc_final: 0.6230 (mtm-85) REVERT: L 138 ARG cc_start: 0.6820 (mmm160) cc_final: 0.6275 (mmm160) outliers start: 57 outliers final: 36 residues processed: 309 average time/residue: 1.6672 time to fit residues: 591.3895 Evaluate side-chains 310 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 258 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 409 ARG Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 5.9990 chunk 315 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 272 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 82 optimal weight: 10.0000 chunk 296 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 304 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 388 ASN D 448 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.121503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.093757 restraints weight = 43930.935| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.76 r_work: 0.3008 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30067 Z= 0.165 Angle : 0.499 7.967 40740 Z= 0.254 Chirality : 0.042 0.253 4567 Planarity : 0.004 0.057 5329 Dihedral : 5.573 128.495 4223 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.69 % Allowed : 17.88 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3761 helix: 1.72 (0.14), residues: 1547 sheet: -0.06 (0.22), residues: 560 loop : -0.05 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 471 HIS 0.004 0.001 HIS C 418 PHE 0.012 0.001 PHE A 230 TYR 0.010 0.001 TYR G 133 ARG 0.014 0.000 ARG C 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10986.87 seconds wall clock time: 195 minutes 25.37 seconds (11725.37 seconds total)