Starting phenix.real_space_refine on Wed Feb 21 02:18:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/02_2024/8gxz_34366_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/02_2024/8gxz_34366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/02_2024/8gxz_34366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/02_2024/8gxz_34366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/02_2024/8gxz_34366_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/02_2024/8gxz_34366_updated.pdb" } resolution = 3.1 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= 0.006 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 3 5.49 5 Mg 1 5.21 5 S 104 5.16 5 C 18715 2.51 5 N 5121 2.21 5 O 5555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 408": "OD1" <-> "OD2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 20": "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: 29499 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: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 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: 14.79, per 1000 atoms: 0.50 Number of scatterers: 29499 At special positions: 0 Unit cell: (147.42, 148.23, 171.72, 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 104 16.00 P 3 15.00 Mg 1 11.99 O 5555 8.00 N 5121 7.00 C 18715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.34 Conformation dependent library (CDL) restraints added in 5.7 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 135 helices and 35 sheets defined 42.4% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.31 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 269 removed outlier: 3.597A pdb=" N THR A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 316 removed outlier: 4.149A 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: 3.976A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 363 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 394 through 400 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 447 through 471 removed outlier: 3.696A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 532 Processing helix chain 'A' and resid 536 through 541 removed outlier: 4.693A pdb=" N GLN A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 552 removed outlier: 4.678A pdb=" N ARG A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 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 269 Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 316 removed outlier: 4.760A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.032A 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 354 through 362 Processing helix chain 'B' and resid 394 through 401 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 Processing helix chain 'B' and resid 447 through 470 removed outlier: 3.741A pdb=" N GLN B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 478 through 493 removed outlier: 3.503A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 532 Processing helix chain 'B' and resid 536 through 541 removed outlier: 4.264A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.751A pdb=" N ALA B 551 " --> pdb=" O ARG B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 575 removed outlier: 4.261A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 572 " --> pdb=" O LYS B 568 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 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 269 Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 296 through 315 removed outlier: 3.808A 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: 3.776A 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 432 through 442 removed outlier: 3.566A pdb=" N ASP C 436 " --> pdb=" O THR C 432 " (cutoff:3.500A) Proline residue: C 437 - end of helix removed outlier: 3.584A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 471 removed outlier: 3.992A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 509 through 531 Processing helix chain 'C' and resid 536 through 540 Processing helix chain 'C' and resid 544 through 548 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 556 through 577 Proline residue: C 560 - end of helix removed outlier: 4.096A pdb=" N GLU C 564 " --> pdb=" O PRO C 560 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 3.969A 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 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 213 through 216 Processing helix chain 'D' and resid 228 through 249 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 287 through 297 removed outlier: 4.303A pdb=" N ARG D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.819A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 403 No H-bonds generated for 'chain 'D' and resid 401 through 403' Processing helix chain 'D' and resid 406 through 421 removed outlier: 3.593A pdb=" N ASP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.645A 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 'D' and resid 467 through 471 removed outlier: 3.560A pdb=" N TRP D 471 " --> pdb=" O GLU D 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 26 No H-bonds generated for 'chain 'E' and resid 24 through 26' 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 121 through 123 No H-bonds generated for 'chain 'E' and resid 121 through 123' Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 198 through 209 Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 228 through 249 removed outlier: 3.785A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 287 through 297 removed outlier: 4.658A 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 332 removed outlier: 3.557A pdb=" N ILE E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 360 through 365 removed outlier: 4.071A pdb=" N ASN E 363 " --> pdb=" O ARG E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 399 removed outlier: 4.179A pdb=" N LYS E 376 " --> pdb=" O GLU E 373 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN E 377 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE E 399 " --> pdb=" O VAL E 396 " (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: 3.806A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 462 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 229 through 249 Proline residue: F 235 - end of helix removed outlier: 3.554A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS F 249 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 274 Processing helix chain 'F' and resid 287 through 297 removed outlier: 3.541A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 345 Processing helix chain 'F' and resid 362 through 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.596A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) 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: 4.057A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 456 through 462 Processing helix chain 'F' and resid 467 through 470 No H-bonds generated for 'chain 'F' and resid 467 through 470' Processing helix chain 'G' and resid 8 through 70 removed outlier: 3.726A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.588A 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 208 removed outlier: 3.822A pdb=" N GLU G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 7 through 15 Processing helix chain 'H' and resid 26 through 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 60 through 65 Processing helix chain 'H' and resid 78 through 82 removed outlier: 3.966A pdb=" N GLN H 82 " --> pdb=" O GLU H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 97 Processing helix chain 'I' and resid 82 through 118 removed outlier: 3.568A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 96 Proline residue: J 95 - end of helix Processing helix chain 'J' and resid 100 through 114 Processing helix chain 'J' and resid 125 through 138 Proline residue: J 129 - end of helix removed outlier: 4.282A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 186 removed outlier: 3.741A pdb=" N LEU J 171 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP J 172 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG J 173 " --> pdb=" O ALA J 169 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 118 removed outlier: 3.676A pdb=" N ARG K 87 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET K 104 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA K 105 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP K 108 " --> pdb=" O ALA K 105 " (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 129 through 138 removed outlier: 4.858A pdb=" N ALA L 133 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 186 removed outlier: 3.799A pdb=" N ASP L 172 " --> pdb=" O LEU L 168 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG L 173 " --> pdb=" O ALA L 169 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2 through 5 removed outlier: 4.163A pdb=" N ILE A 2 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.690A 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 76 Processing sheet with id= C, first strand: chain 'A' and resid 164 through 166 removed outlier: 5.677A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.747A pdb=" N ARG A 197 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS A 367 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 249 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N MET A 323 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 251 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 223 through 227 removed outlier: 6.313A pdb=" N ILE A 380 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE A 226 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLY A 382 " --> pdb=" O ILE A 226 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.924A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 2 through 5 removed outlier: 4.392A pdb=" N ILE B 2 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 72 through 75 Processing sheet with id= I, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.839A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 223 through 227 removed outlier: 8.698A pdb=" N ALA B 224 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE B 380 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE B 226 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY B 382 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASP B 325 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 253 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 366 through 369 removed outlier: 3.546A pdb=" N VAL B 378 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.671A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.467A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 72 through 76 Processing sheet with id= O, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.257A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) 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 366 through 369 Processing sheet with id= R, first strand: chain 'C' and resid 134 through 139 removed outlier: 6.658A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.682A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL C 160 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL C 172 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU C 181 " --> pdb=" O VAL C 172 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.382A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.655A 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 removed outlier: 3.564A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 91 through 93 removed outlier: 4.192A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.515A pdb=" N LEU D 314 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 11 through 15 removed outlier: 3.517A pdb=" N THR E 12 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 81 through 84 Processing sheet with id= Z, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= AA, first strand: chain 'E' and resid 307 through 310 removed outlier: 3.583A pdb=" N MET E 194 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 72 through 77 removed outlier: 6.838A pdb=" N ILE F 32 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL F 56 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.815A pdb=" N ARG F 91 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AE, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.416A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 91 through 96 removed outlier: 3.508A pdb=" N SER G 99 " --> pdb=" O VAL G 96 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 19 through 23 removed outlier: 3.500A pdb=" N ALA H 5 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ASP H 6 " --> pdb=" O ASP H 48 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 141 through 144 removed outlier: 3.846A pdb=" N GLU J 141 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA J 123 " --> pdb=" O GLN J 143 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 120 through 122 removed outlier: 3.779A pdb=" N ALA L 120 " --> pdb=" O VAL L 155 " (cutoff:3.500A) 1227 hydrogen bonds defined for protein. 3165 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.46 Time building geometry restraints manager: 13.17 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: 9960 1.34 - 1.46: 4580 1.46 - 1.57: 15313 1.57 - 1.69: 5 1.69 - 1.81: 194 Bond restraints: 30052 Sorted by residual: bond pdb=" CB ARG C 95 " pdb=" CG ARG C 95 " ideal model delta sigma weight residual 1.520 1.399 0.121 3.00e-02 1.11e+03 1.62e+01 bond pdb=" CG ARG C 95 " pdb=" CD ARG C 95 " ideal model delta sigma weight residual 1.520 1.405 0.115 3.00e-02 1.11e+03 1.47e+01 bond pdb=" O4 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.455 0.044 2.00e-02 2.50e+03 4.90e+00 bond pdb=" O3 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.455 0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" CA ARG C 95 " pdb=" CB ARG C 95 " ideal model delta sigma weight residual 1.531 1.498 0.034 1.57e-02 4.06e+03 4.60e+00 ... (remaining 30047 not shown) Histogram of bond angle deviations from ideal: 99.81 - 107.78: 1258 107.78 - 115.76: 18399 115.76 - 123.74: 20356 123.74 - 131.72: 664 131.72 - 139.70: 39 Bond angle restraints: 40716 Sorted by residual: angle pdb=" CG ARG C 95 " pdb=" CD ARG C 95 " pdb=" NE ARG C 95 " ideal model delta sigma weight residual 112.00 104.50 7.50 2.20e+00 2.07e-01 1.16e+01 angle pdb=" N HIS E 375 " pdb=" CA HIS E 375 " pdb=" C HIS E 375 " ideal model delta sigma weight residual 111.07 114.08 -3.01 1.07e+00 8.73e-01 7.89e+00 angle pdb=" N ILE F 100 " pdb=" CA ILE F 100 " pdb=" C ILE F 100 " ideal model delta sigma weight residual 113.20 110.56 2.64 9.60e-01 1.09e+00 7.54e+00 angle pdb=" C2' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O3' ATP C 601 " ideal model delta sigma weight residual 111.83 104.97 6.86 2.67e+00 1.40e-01 6.61e+00 angle pdb=" C GLU B 347 " pdb=" CA GLU B 347 " pdb=" CB GLU B 347 " ideal model delta sigma weight residual 110.42 115.22 -4.80 1.99e+00 2.53e-01 5.81e+00 ... (remaining 40711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 16690 17.91 - 35.82: 1335 35.82 - 53.73: 217 53.73 - 71.63: 57 71.63 - 89.54: 39 Dihedral angle restraints: 18338 sinusoidal: 7516 harmonic: 10822 Sorted by residual: dihedral pdb=" CA LEU F 257 " pdb=" C LEU F 257 " pdb=" N THR F 258 " pdb=" CA THR F 258 " ideal model delta harmonic sigma weight residual 180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU D 257 " pdb=" C LEU D 257 " pdb=" N THR D 258 " pdb=" CA THR D 258 " ideal model delta harmonic sigma weight residual 180.00 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU L 128 " pdb=" C LEU L 128 " pdb=" N PRO L 129 " pdb=" CA PRO L 129 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 18335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3899 0.058 - 0.116: 593 0.116 - 0.174: 69 0.174 - 0.232: 0 0.232 - 0.290: 3 Chirality restraints: 4564 Sorted by residual: chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' ATP C 601 " pdb=" C2' ATP C 601 " pdb=" C4' ATP C 601 " pdb=" O3' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C4' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" C5' ATP C 601 " pdb=" O4' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.73 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 4561 not shown) Planarity restraints: 5331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 393 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 394 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 355 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO D 356 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 356 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 356 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 229 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " 0.022 5.00e-02 4.00e+02 ... (remaining 5328 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 118 2.44 - 3.06: 20636 3.06 - 3.67: 42792 3.67 - 4.29: 64635 4.29 - 4.90: 111334 Nonbonded interactions: 239515 Sorted by model distance: nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 1.826 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 1.888 2.170 nonbonded pdb=" O3B ATP C 601 " pdb="MG MG C 602 " model vdw 1.893 2.170 nonbonded pdb=" OG SER H 24 " pdb=" OE1 GLU H 28 " model vdw 1.939 2.440 nonbonded pdb=" O LYS D 370 " pdb=" OG1 THR D 371 " model vdw 1.953 2.440 ... (remaining 239510 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 578) selection = chain 'B' selection = (chain 'C' and resid 1 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 6.440 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 79.390 Find NCS groups from input model: 1.910 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 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 : 0.006 0.121 30052 Z= 0.371 Angle : 0.536 7.501 40716 Z= 0.283 Chirality : 0.043 0.290 4564 Planarity : 0.004 0.058 5331 Dihedral : 13.924 89.543 11420 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3764 helix: 1.46 (0.13), residues: 1571 sheet: -1.06 (0.21), residues: 594 loop : -0.19 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 175 HIS 0.004 0.001 HIS B 145 PHE 0.018 0.001 PHE A 269 TYR 0.021 0.001 TYR D 331 ARG 0.004 0.000 ARG E 174 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 823 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 95 ARG cc_start: 0.6391 (tpt-90) cc_final: 0.6012 (tpt-90) REVERT: A 96 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6398 (pt0) REVERT: A 129 VAL cc_start: 0.7083 (t) cc_final: 0.6662 (m) REVERT: A 143 PHE cc_start: 0.7299 (m-80) cc_final: 0.6979 (m-80) REVERT: A 156 ARG cc_start: 0.5953 (mtp-110) cc_final: 0.5209 (ttp-170) REVERT: A 174 VAL cc_start: 0.7585 (t) cc_final: 0.7216 (p) REVERT: A 182 LYS cc_start: 0.6738 (mtmm) cc_final: 0.6368 (mptt) REVERT: A 323 MET cc_start: 0.8377 (mmt) cc_final: 0.8068 (mmm) REVERT: A 337 ILE cc_start: 0.7042 (mm) cc_final: 0.6587 (mt) REVERT: A 340 ARG cc_start: 0.6537 (tpp-160) cc_final: 0.5995 (mpt180) REVERT: A 348 GLU cc_start: 0.7167 (mt-10) cc_final: 0.5920 (tt0) REVERT: A 374 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6043 (tt0) REVERT: A 375 GLU cc_start: 0.6368 (tt0) cc_final: 0.6057 (tt0) REVERT: A 416 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.6309 (mtp85) REVERT: A 481 ARG cc_start: 0.7125 (mtm-85) cc_final: 0.6650 (mtp-110) REVERT: A 492 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6996 (tt0) REVERT: A 517 LYS cc_start: 0.6952 (mmtp) cc_final: 0.6710 (mtpt) REVERT: A 518 MET cc_start: 0.8303 (mtp) cc_final: 0.8051 (mtm) REVERT: A 541 GLN cc_start: 0.6311 (mt0) cc_final: 0.5858 (pt0) REVERT: A 546 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6170 (mm-30) REVERT: A 550 ARG cc_start: 0.6935 (mtm-85) cc_final: 0.6555 (tpp-160) REVERT: A 557 GLU cc_start: 0.7214 (pm20) cc_final: 0.6413 (tp30) REVERT: A 558 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7085 (mt-10) REVERT: A 565 GLU cc_start: 0.7347 (tp30) cc_final: 0.6834 (mt-10) REVERT: A 567 MET cc_start: 0.6993 (mmm) cc_final: 0.6690 (mmm) REVERT: B 3 GLN cc_start: 0.7514 (tt0) cc_final: 0.6932 (mt0) REVERT: B 29 LYS cc_start: 0.7039 (mtpt) cc_final: 0.6664 (mttt) REVERT: B 59 LYS cc_start: 0.7602 (mtpp) cc_final: 0.7089 (mttp) REVERT: B 93 ARG cc_start: 0.6342 (mtm-85) cc_final: 0.6125 (mtm180) REVERT: B 130 ARG cc_start: 0.5639 (ttm-80) cc_final: 0.5288 (tpt170) REVERT: B 133 MET cc_start: 0.6094 (mmm) cc_final: 0.5823 (mmt) REVERT: B 134 VAL cc_start: 0.7311 (m) cc_final: 0.7072 (t) REVERT: B 159 GLU cc_start: 0.7268 (tt0) cc_final: 0.6060 (tp30) REVERT: B 166 TYR cc_start: 0.7004 (m-10) cc_final: 0.5893 (m-80) REVERT: B 197 ARG cc_start: 0.6468 (ttp80) cc_final: 0.6115 (ttp-110) REVERT: B 200 ASP cc_start: 0.6602 (m-30) cc_final: 0.6366 (m-30) REVERT: B 220 MET cc_start: 0.7641 (tpp) cc_final: 0.7379 (ttm) REVERT: B 236 VAL cc_start: 0.7230 (t) cc_final: 0.7006 (p) REVERT: B 243 LYS cc_start: 0.7176 (mtpp) cc_final: 0.6917 (mtpp) REVERT: B 264 ASP cc_start: 0.6515 (m-30) cc_final: 0.6230 (m-30) REVERT: B 340 ARG cc_start: 0.6820 (tpp-160) cc_final: 0.6513 (tpt-90) REVERT: B 374 GLU cc_start: 0.6185 (mt-10) cc_final: 0.5722 (mm-30) REVERT: B 480 GLU cc_start: 0.6331 (mp0) cc_final: 0.5936 (mt-10) REVERT: B 481 ARG cc_start: 0.6785 (mmm-85) cc_final: 0.5968 (mmm160) REVERT: B 553 TYR cc_start: 0.7670 (m-10) cc_final: 0.7419 (m-10) REVERT: C 5 VAL cc_start: 0.8148 (t) cc_final: 0.7911 (m) REVERT: C 24 MET cc_start: 0.8053 (mtp) cc_final: 0.7730 (mmm) REVERT: C 69 LEU cc_start: 0.7718 (mt) cc_final: 0.7448 (mp) REVERT: C 84 TYR cc_start: 0.8652 (m-80) cc_final: 0.8437 (m-80) REVERT: C 124 LYS cc_start: 0.7262 (mttt) cc_final: 0.6930 (mtmm) REVERT: C 125 PRO cc_start: 0.7245 (Cg_exo) cc_final: 0.6763 (Cg_endo) REVERT: C 183 MET cc_start: 0.8416 (mtp) cc_final: 0.8203 (mtm) REVERT: C 191 ARG cc_start: 0.7840 (mtp180) cc_final: 0.7503 (ttp80) REVERT: C 197 ARG cc_start: 0.7495 (mtm110) cc_final: 0.7275 (ptm-80) REVERT: C 198 LYS cc_start: 0.7288 (mmtp) cc_final: 0.7047 (mmmt) REVERT: C 268 GLU cc_start: 0.6702 (mt-10) cc_final: 0.5867 (tp30) REVERT: C 272 LEU cc_start: 0.7520 (mt) cc_final: 0.7316 (mt) REVERT: C 338 SER cc_start: 0.7704 (t) cc_final: 0.7232 (p) REVERT: C 344 MET cc_start: 0.7786 (mmm) cc_final: 0.7529 (mmt) REVERT: C 367 LYS cc_start: 0.7633 (ttpp) cc_final: 0.7269 (ttpp) REVERT: C 374 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6663 (mm-30) REVERT: C 393 GLU cc_start: 0.6565 (tm-30) cc_final: 0.6317 (tm-30) REVERT: C 416 ARG cc_start: 0.7325 (mtm110) cc_final: 0.6653 (mtm180) REVERT: C 442 ASN cc_start: 0.8212 (m-40) cc_final: 0.7812 (m-40) REVERT: C 452 ASP cc_start: 0.7241 (m-30) cc_final: 0.6879 (m-30) REVERT: C 460 ARG cc_start: 0.7080 (mtm180) cc_final: 0.6850 (mtm-85) REVERT: C 513 TYR cc_start: 0.7369 (t80) cc_final: 0.6959 (t80) REVERT: C 518 MET cc_start: 0.7998 (mtp) cc_final: 0.7693 (mtm) REVERT: C 524 LYS cc_start: 0.6951 (mtpp) cc_final: 0.6547 (ttpp) REVERT: C 525 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6234 (mt-10) REVERT: C 547 ARG cc_start: 0.6217 (mtp85) cc_final: 0.5803 (mtp85) REVERT: C 550 ARG cc_start: 0.6744 (ttm-80) cc_final: 0.6400 (mtm110) REVERT: D 22 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6928 (mt-10) REVERT: D 51 SER cc_start: 0.7670 (t) cc_final: 0.7406 (p) REVERT: D 52 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7075 (mt-10) REVERT: D 92 ARG cc_start: 0.7576 (mtm110) cc_final: 0.6990 (mtm-85) REVERT: D 111 ARG cc_start: 0.7359 (mtp-110) cc_final: 0.7026 (mmm-85) REVERT: D 199 ARG cc_start: 0.6475 (ttp80) cc_final: 0.6116 (ttp80) REVERT: D 231 ARG cc_start: 0.7450 (ttm170) cc_final: 0.7236 (ttm170) REVERT: D 232 ILE cc_start: 0.7456 (mm) cc_final: 0.7174 (mt) REVERT: D 250 ASP cc_start: 0.7756 (m-30) cc_final: 0.7547 (m-30) REVERT: D 269 GLU cc_start: 0.6088 (tt0) cc_final: 0.5757 (mt-10) REVERT: D 280 ARG cc_start: 0.7016 (mtp85) cc_final: 0.6387 (mtp-110) REVERT: D 302 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6552 (mm-30) REVERT: D 305 LYS cc_start: 0.6868 (mtmm) cc_final: 0.6115 (mtpp) REVERT: D 337 ILE cc_start: 0.8288 (mt) cc_final: 0.8076 (mm) REVERT: D 338 GLN cc_start: 0.8540 (tt0) cc_final: 0.8031 (tp40) REVERT: D 376 LYS cc_start: 0.6549 (tppt) cc_final: 0.5787 (tttm) REVERT: D 406 GLU cc_start: 0.6061 (tp30) cc_final: 0.5379 (pm20) REVERT: D 409 ARG cc_start: 0.6647 (ttm-80) cc_final: 0.6269 (mtt90) REVERT: D 416 ASP cc_start: 0.7040 (t0) cc_final: 0.6240 (m-30) REVERT: D 461 LYS cc_start: 0.6961 (tttt) cc_final: 0.6754 (ttmt) REVERT: D 463 TYR cc_start: 0.7646 (t80) cc_final: 0.7394 (t80) REVERT: D 465 GLN cc_start: 0.6690 (mm-40) cc_final: 0.6374 (mp10) REVERT: E 25 LYS cc_start: 0.7336 (ttmm) cc_final: 0.7055 (mtpp) REVERT: E 128 GLU cc_start: 0.7079 (pt0) cc_final: 0.6701 (pt0) REVERT: E 228 THR cc_start: 0.8009 (t) cc_final: 0.7392 (m) REVERT: E 251 TYR cc_start: 0.7793 (m-80) cc_final: 0.7274 (m-80) REVERT: E 252 HIS cc_start: 0.8169 (m-70) cc_final: 0.7881 (m170) REVERT: E 302 GLU cc_start: 0.6980 (tt0) cc_final: 0.5904 (tp30) REVERT: E 345 ARG cc_start: 0.6305 (mtm110) cc_final: 0.6068 (mtm-85) REVERT: E 394 LYS cc_start: 0.6768 (tptp) cc_final: 0.6283 (tttm) REVERT: E 410 ARG cc_start: 0.4761 (mtm180) cc_final: 0.4097 (mmp80) REVERT: E 420 ARG cc_start: 0.7440 (mtm110) cc_final: 0.7236 (mtm-85) REVERT: E 445 MET cc_start: 0.7298 (mtp) cc_final: 0.7016 (mtt) REVERT: E 450 GLU cc_start: 0.5914 (mm-30) cc_final: 0.5698 (mt-10) REVERT: F 6 LYS cc_start: 0.6096 (tptm) cc_final: 0.5689 (mtpp) REVERT: F 7 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6813 (mt-10) REVERT: F 13 TYR cc_start: 0.8585 (t80) cc_final: 0.8252 (t80) REVERT: F 53 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6390 (mm-30) REVERT: F 77 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6940 (pt0) REVERT: F 81 ARG cc_start: 0.7387 (mtt-85) cc_final: 0.6880 (mtm-85) REVERT: F 98 LYS cc_start: 0.7429 (mttt) cc_final: 0.7055 (mmtm) REVERT: F 207 GLU cc_start: 0.6592 (mm-30) cc_final: 0.5996 (tm-30) REVERT: F 209 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6725 (mt-10) REVERT: F 210 ARG cc_start: 0.6282 (ttp80) cc_final: 0.5322 (ttm110) REVERT: F 230 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6928 (mt-10) REVERT: F 280 ARG cc_start: 0.7680 (mtp85) cc_final: 0.7365 (mtt180) REVERT: F 302 GLU cc_start: 0.7292 (tt0) cc_final: 0.6717 (mm-30) REVERT: F 305 LYS cc_start: 0.7994 (mttt) cc_final: 0.7787 (mttm) REVERT: F 362 MET cc_start: 0.8007 (ttp) cc_final: 0.7771 (ttt) REVERT: F 409 ARG cc_start: 0.6795 (ttm110) cc_final: 0.6117 (mtt90) REVERT: F 412 LEU cc_start: 0.7402 (tp) cc_final: 0.7183 (tp) REVERT: F 453 ARG cc_start: 0.6971 (mmt90) cc_final: 0.6716 (mmm-85) REVERT: G 17 GLN cc_start: 0.6886 (mm-40) cc_final: 0.6570 (mm-40) REVERT: G 38 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6467 (tp30) REVERT: G 47 MET cc_start: 0.5255 (mmm) cc_final: 0.4213 (ttm) REVERT: G 177 ARG cc_start: 0.6645 (mtp85) cc_final: 0.6267 (mtm-85) REVERT: G 180 GLN cc_start: 0.7189 (mt0) cc_final: 0.6964 (mt0) REVERT: G 198 LYS cc_start: 0.6461 (tttm) cc_final: 0.6256 (ttmm) REVERT: H 63 MET cc_start: 0.3761 (mmm) cc_final: 0.2141 (ttp) REVERT: J 65 GLU cc_start: 0.4107 (mt-10) cc_final: 0.3655 (mm-30) REVERT: J 86 ARG cc_start: 0.4035 (mmp80) cc_final: 0.3396 (ttm-80) REVERT: J 105 ARG cc_start: 0.3493 (mtt-85) cc_final: 0.3235 (mtt-85) REVERT: J 112 LEU cc_start: 0.4601 (mp) cc_final: 0.4061 (tt) REVERT: J 158 GLU cc_start: 0.5277 (mp0) cc_final: 0.4537 (mt-10) REVERT: J 182 VAL cc_start: 0.3334 (t) cc_final: 0.3066 (p) REVERT: L 86 ARG cc_start: 0.5163 (mtt180) cc_final: 0.4852 (mtp180) REVERT: L 102 GLU cc_start: 0.5661 (mp0) cc_final: 0.4687 (tp30) REVERT: L 153 ARG cc_start: 0.3855 (ttm170) cc_final: 0.3545 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 823 average time/residue: 0.5168 time to fit residues: 617.4345 Evaluate side-chains 506 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 chunk 156 optimal weight: 0.6980 chunk 96 optimal weight: 0.1980 chunk 190 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 292 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 217 optimal weight: 0.8980 chunk 338 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 442 ASN A 571 GLN B 145 HIS B 571 GLN C 81 ASN C 283 HIS ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 HIS C 459 GLN C 496 GLN D 252 HIS ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 HIS D 448 GLN E 58 GLN E 148 GLN E 198 GLN E 249 HIS ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN F 206 GLN F 388 ASN F 413 GLN F 427 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 30052 Z= 0.217 Angle : 0.541 9.608 40716 Z= 0.284 Chirality : 0.044 0.198 4564 Planarity : 0.005 0.042 5331 Dihedral : 5.020 84.899 4214 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.64 % Rotamer: Outliers : 1.39 % Allowed : 9.70 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.14), residues: 3764 helix: 1.39 (0.13), residues: 1583 sheet: -0.68 (0.22), residues: 587 loop : 0.12 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 175 HIS 0.004 0.001 HIS C 283 PHE 0.014 0.001 PHE F 414 TYR 0.013 0.001 TYR H 89 ARG 0.014 0.001 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 515 time to evaluate : 3.337 Fit side-chains REVERT: A 7 GLN cc_start: 0.8619 (tt0) cc_final: 0.8392 (tt0) REVERT: A 62 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7565 (mt-10) REVERT: A 95 ARG cc_start: 0.6567 (tpt-90) cc_final: 0.5969 (tpt-90) REVERT: A 96 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6376 (pt0) REVERT: A 143 PHE cc_start: 0.7377 (m-80) cc_final: 0.7172 (m-80) REVERT: A 154 ARG cc_start: 0.7049 (mtp85) cc_final: 0.6767 (mtp85) REVERT: A 156 ARG cc_start: 0.6024 (mtp-110) cc_final: 0.5246 (ttp-170) REVERT: A 169 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6960 (mm-30) REVERT: A 174 VAL cc_start: 0.7654 (t) cc_final: 0.7341 (p) REVERT: A 182 LYS cc_start: 0.6722 (mtmm) cc_final: 0.6360 (mptt) REVERT: A 257 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7324 (mm-30) REVERT: A 262 MET cc_start: 0.7523 (mmp) cc_final: 0.6882 (mmt) REVERT: A 337 ILE cc_start: 0.7091 (mm) cc_final: 0.6594 (mt) REVERT: A 340 ARG cc_start: 0.6542 (tpp-160) cc_final: 0.5923 (mpt180) REVERT: A 348 GLU cc_start: 0.7215 (mt-10) cc_final: 0.5820 (tt0) REVERT: A 374 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6037 (tt0) REVERT: A 375 GLU cc_start: 0.6661 (tt0) cc_final: 0.6229 (mt-10) REVERT: A 416 ARG cc_start: 0.7409 (mtm-85) cc_final: 0.6372 (mtp85) REVERT: A 481 ARG cc_start: 0.7177 (mtm-85) cc_final: 0.6585 (mtp-110) REVERT: A 492 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6304 (pt0) REVERT: A 517 LYS cc_start: 0.7019 (mmtp) cc_final: 0.6782 (mtpt) REVERT: A 518 MET cc_start: 0.8321 (mtp) cc_final: 0.8115 (mtp) REVERT: A 541 GLN cc_start: 0.6482 (mt0) cc_final: 0.5847 (pt0) REVERT: A 546 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6095 (mm-30) REVERT: A 547 ARG cc_start: 0.6709 (ttm110) cc_final: 0.6112 (ttm110) REVERT: A 550 ARG cc_start: 0.6941 (mtm-85) cc_final: 0.6592 (tpp-160) REVERT: A 557 GLU cc_start: 0.7219 (pm20) cc_final: 0.6433 (tp30) REVERT: A 567 MET cc_start: 0.7112 (mmm) cc_final: 0.6885 (mmm) REVERT: B 29 LYS cc_start: 0.7079 (mtpt) cc_final: 0.6755 (mttt) REVERT: B 134 VAL cc_start: 0.7401 (m) cc_final: 0.7154 (t) REVERT: B 159 GLU cc_start: 0.7279 (tt0) cc_final: 0.6043 (tp30) REVERT: B 166 TYR cc_start: 0.7011 (m-10) cc_final: 0.5907 (m-80) REVERT: B 197 ARG cc_start: 0.6502 (ttp80) cc_final: 0.6250 (ttp-110) REVERT: B 220 MET cc_start: 0.7675 (tpp) cc_final: 0.7334 (ttm) REVERT: B 241 LEU cc_start: 0.7648 (mp) cc_final: 0.7269 (tt) REVERT: B 243 LYS cc_start: 0.7290 (mtpp) cc_final: 0.7016 (mtpt) REVERT: B 340 ARG cc_start: 0.6728 (tpp-160) cc_final: 0.6414 (tpt-90) REVERT: B 374 GLU cc_start: 0.6383 (mt-10) cc_final: 0.5842 (mm-30) REVERT: B 384 VAL cc_start: 0.7904 (t) cc_final: 0.7541 (m) REVERT: B 449 GLU cc_start: 0.6264 (mm-30) cc_final: 0.5667 (mp0) REVERT: B 480 GLU cc_start: 0.6535 (mp0) cc_final: 0.5872 (mt-10) REVERT: B 481 ARG cc_start: 0.6959 (mmm-85) cc_final: 0.6372 (ttt-90) REVERT: B 553 TYR cc_start: 0.7729 (m-10) cc_final: 0.7371 (m-10) REVERT: C 101 TYR cc_start: 0.7943 (m-80) cc_final: 0.7297 (m-80) REVERT: C 124 LYS cc_start: 0.7400 (mttt) cc_final: 0.7185 (mtmm) REVERT: C 130 ARG cc_start: 0.6525 (ttp-110) cc_final: 0.5736 (tpp-160) REVERT: C 183 MET cc_start: 0.8527 (mtp) cc_final: 0.8234 (mtm) REVERT: C 191 ARG cc_start: 0.7776 (mtp180) cc_final: 0.7422 (ttp80) REVERT: C 197 ARG cc_start: 0.7458 (mtm110) cc_final: 0.7105 (ptm-80) REVERT: C 198 LYS cc_start: 0.7322 (mmtp) cc_final: 0.7119 (mmmt) REVERT: C 338 SER cc_start: 0.7863 (t) cc_final: 0.7449 (p) REVERT: C 367 LYS cc_start: 0.7655 (ttpp) cc_final: 0.7168 (ttmt) REVERT: C 374 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6545 (mm-30) REVERT: C 416 ARG cc_start: 0.7209 (mtm110) cc_final: 0.6475 (mtm180) REVERT: C 442 ASN cc_start: 0.8256 (m-40) cc_final: 0.7748 (m-40) REVERT: C 452 ASP cc_start: 0.7239 (m-30) cc_final: 0.6970 (m-30) REVERT: C 518 MET cc_start: 0.7967 (mtp) cc_final: 0.7660 (mtm) REVERT: C 524 LYS cc_start: 0.7066 (mtpp) cc_final: 0.6821 (ttpp) REVERT: C 525 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6328 (mt-10) REVERT: C 547 ARG cc_start: 0.6264 (mtp85) cc_final: 0.5926 (mtp180) REVERT: C 550 ARG cc_start: 0.6812 (ttm-80) cc_final: 0.6525 (mtm110) REVERT: D 22 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6192 (mm-30) REVERT: D 34 ASP cc_start: 0.7087 (m-30) cc_final: 0.6606 (t0) REVERT: D 52 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6680 (mt-10) REVERT: D 111 ARG cc_start: 0.7316 (mtp-110) cc_final: 0.7111 (mmm-85) REVERT: D 231 ARG cc_start: 0.7574 (ttm170) cc_final: 0.7218 (ttp-110) REVERT: D 269 GLU cc_start: 0.6168 (tt0) cc_final: 0.5794 (mt-10) REVERT: D 280 ARG cc_start: 0.7031 (mtp85) cc_final: 0.6331 (mtp-110) REVERT: D 302 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6645 (mm-30) REVERT: D 305 LYS cc_start: 0.6944 (mtmm) cc_final: 0.5578 (tttt) REVERT: D 331 TYR cc_start: 0.7137 (m-10) cc_final: 0.6931 (m-10) REVERT: D 338 GLN cc_start: 0.8472 (tt0) cc_final: 0.7875 (tp40) REVERT: D 406 GLU cc_start: 0.5813 (tp30) cc_final: 0.5278 (pm20) REVERT: D 409 ARG cc_start: 0.6574 (ttm-80) cc_final: 0.6154 (mtt90) REVERT: D 437 GLN cc_start: 0.7526 (tt0) cc_final: 0.7233 (tt0) REVERT: D 461 LYS cc_start: 0.6923 (tttt) cc_final: 0.6535 (tttp) REVERT: D 463 TYR cc_start: 0.7694 (t80) cc_final: 0.6915 (t80) REVERT: E 110 LYS cc_start: 0.6966 (ttmm) cc_final: 0.6359 (mtpp) REVERT: E 128 GLU cc_start: 0.7167 (pt0) cc_final: 0.6779 (pt0) REVERT: E 130 PHE cc_start: 0.7662 (t80) cc_final: 0.7404 (t80) REVERT: E 194 MET cc_start: 0.8570 (mtm) cc_final: 0.8299 (mtm) REVERT: E 209 GLU cc_start: 0.5870 (mt-10) cc_final: 0.5488 (mm-30) REVERT: E 219 LEU cc_start: 0.7527 (mt) cc_final: 0.7297 (mp) REVERT: E 228 THR cc_start: 0.7975 (t) cc_final: 0.7700 (m) REVERT: E 252 HIS cc_start: 0.8257 (m-70) cc_final: 0.7993 (m170) REVERT: E 259 ASP cc_start: 0.6261 (m-30) cc_final: 0.5770 (m-30) REVERT: E 302 GLU cc_start: 0.6852 (tt0) cc_final: 0.5754 (tp30) REVERT: E 305 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7584 (mtpp) REVERT: E 360 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6599 (mtt-85) REVERT: E 420 ARG cc_start: 0.7412 (mtm110) cc_final: 0.7206 (mtm-85) REVERT: E 445 MET cc_start: 0.7327 (mtp) cc_final: 0.6982 (mtt) REVERT: F 6 LYS cc_start: 0.6087 (tptm) cc_final: 0.5770 (mtpp) REVERT: F 7 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6741 (mt-10) REVERT: F 53 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6666 (pt0) REVERT: F 77 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7002 (pt0) REVERT: F 86 LYS cc_start: 0.7364 (tptp) cc_final: 0.6954 (tptm) REVERT: F 98 LYS cc_start: 0.7282 (mttt) cc_final: 0.6955 (mmtp) REVERT: F 207 GLU cc_start: 0.6692 (mm-30) cc_final: 0.6123 (tm-30) REVERT: F 209 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6478 (mt-10) REVERT: F 210 ARG cc_start: 0.6117 (ttp80) cc_final: 0.5154 (ttm110) REVERT: F 280 ARG cc_start: 0.7634 (mtp85) cc_final: 0.7327 (mtt180) REVERT: F 302 GLU cc_start: 0.7378 (tt0) cc_final: 0.6738 (mm-30) REVERT: F 362 MET cc_start: 0.8122 (ttp) cc_final: 0.7788 (ttt) REVERT: F 399 ILE cc_start: 0.6494 (mm) cc_final: 0.6026 (mt) REVERT: F 409 ARG cc_start: 0.6848 (ttm110) cc_final: 0.6324 (mtm-85) REVERT: G 9 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6263 (ptm) REVERT: G 47 MET cc_start: 0.4987 (mmm) cc_final: 0.4539 (ttm) REVERT: G 59 GLU cc_start: 0.5345 (pp20) cc_final: 0.4147 (tp30) REVERT: G 177 ARG cc_start: 0.6479 (mtp85) cc_final: 0.6170 (mtm-85) REVERT: G 180 GLN cc_start: 0.7125 (mt0) cc_final: 0.6832 (mt0) REVERT: G 197 ILE cc_start: 0.5203 (pt) cc_final: 0.4965 (mm) REVERT: H 63 MET cc_start: 0.3754 (mmm) cc_final: 0.2202 (ttp) REVERT: J 65 GLU cc_start: 0.4099 (mt-10) cc_final: 0.3713 (tt0) REVERT: J 81 GLU cc_start: 0.4398 (tt0) cc_final: 0.4001 (tp30) REVERT: J 86 ARG cc_start: 0.4154 (mmp80) cc_final: 0.3523 (ttm-80) REVERT: J 112 LEU cc_start: 0.4588 (mp) cc_final: 0.4076 (tt) REVERT: J 164 GLU cc_start: 0.5047 (tp30) cc_final: 0.4522 (mt-10) REVERT: J 173 ARG cc_start: 0.3703 (mtp180) cc_final: 0.3501 (ttt180) REVERT: K 102 LYS cc_start: 0.5369 (tptp) cc_final: 0.3929 (mmtt) REVERT: L 86 ARG cc_start: 0.4972 (mtt180) cc_final: 0.4674 (mtp180) REVERT: L 102 GLU cc_start: 0.5485 (mp0) cc_final: 0.4518 (tp30) REVERT: L 138 ARG cc_start: 0.4360 (mtt180) cc_final: 0.3635 (mtt90) REVERT: L 141 GLU cc_start: 0.4947 (tt0) cc_final: 0.4173 (mm-30) REVERT: L 153 ARG cc_start: 0.3950 (ttm170) cc_final: 0.3370 (ttm-80) outliers start: 43 outliers final: 31 residues processed: 543 average time/residue: 0.5292 time to fit residues: 419.6805 Evaluate side-chains 486 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 453 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 413 GLN Chi-restraints excluded: chain G residue 9 MET 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: 2.9990 chunk 281 optimal weight: 8.9990 chunk 230 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 339 optimal weight: 8.9990 chunk 366 optimal weight: 20.0000 chunk 302 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN A 498 ASN B 185 HIS C 316 GLN ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN D 323 HIS E 364 ASN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS F 249 HIS F 381 GLN G 68 GLN G 180 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.152 30052 Z= 0.523 Angle : 0.746 12.377 40716 Z= 0.386 Chirality : 0.052 0.251 4564 Planarity : 0.007 0.061 5331 Dihedral : 5.826 70.959 4214 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.63 % Rotamer: Outliers : 2.98 % Allowed : 11.55 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 3764 helix: 0.45 (0.13), residues: 1553 sheet: -0.86 (0.20), residues: 595 loop : -0.25 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP J 175 HIS 0.011 0.002 HIS D 375 PHE 0.024 0.003 PHE H 81 TYR 0.021 0.003 TYR B 304 ARG 0.012 0.001 ARG C 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 467 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7403 (mt-10) REVERT: A 93 ARG cc_start: 0.7150 (mmm160) cc_final: 0.6779 (mpt180) REVERT: A 95 ARG cc_start: 0.6462 (tpt-90) cc_final: 0.5748 (tpt-90) REVERT: A 119 TRP cc_start: 0.8190 (OUTLIER) cc_final: 0.6838 (t-100) REVERT: A 154 ARG cc_start: 0.7130 (mtp85) cc_final: 0.6879 (mtp180) REVERT: A 156 ARG cc_start: 0.6102 (mtp-110) cc_final: 0.5248 (ttp-170) REVERT: A 169 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7104 (mm-30) REVERT: A 174 VAL cc_start: 0.7591 (t) cc_final: 0.7231 (p) REVERT: A 257 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7468 (mm-30) REVERT: A 332 GLU cc_start: 0.6621 (mt-10) cc_final: 0.6236 (mt-10) REVERT: A 340 ARG cc_start: 0.6740 (tpp-160) cc_final: 0.5910 (mpt180) REVERT: A 354 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6623 (tp) REVERT: A 374 GLU cc_start: 0.6771 (mt-10) cc_final: 0.5970 (tt0) REVERT: A 416 ARG cc_start: 0.7520 (mtm-85) cc_final: 0.6441 (mtp85) REVERT: A 481 ARG cc_start: 0.7201 (mtm-85) cc_final: 0.6743 (mtp-110) REVERT: A 517 LYS cc_start: 0.7063 (mmtp) cc_final: 0.6803 (mtpt) REVERT: A 518 MET cc_start: 0.8240 (mtp) cc_final: 0.7986 (mtm) REVERT: A 541 GLN cc_start: 0.6283 (mt0) cc_final: 0.5792 (pt0) REVERT: A 546 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6124 (mm-30) REVERT: A 550 ARG cc_start: 0.7154 (mtm-85) cc_final: 0.6655 (tpp-160) REVERT: A 557 GLU cc_start: 0.7268 (pm20) cc_final: 0.6602 (tp30) REVERT: B 119 TRP cc_start: 0.7043 (t60) cc_final: 0.6781 (t60) REVERT: B 128 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6157 (tm-30) REVERT: B 134 VAL cc_start: 0.7425 (m) cc_final: 0.7075 (t) REVERT: B 154 ARG cc_start: 0.6633 (ptp90) cc_final: 0.6079 (ptp90) REVERT: B 166 TYR cc_start: 0.7208 (m-80) cc_final: 0.6118 (m-80) REVERT: B 197 ARG cc_start: 0.6665 (ttp80) cc_final: 0.6187 (ttp-110) REVERT: B 241 LEU cc_start: 0.7654 (mp) cc_final: 0.7275 (tt) REVERT: B 340 ARG cc_start: 0.6861 (tpp-160) cc_final: 0.6542 (tpt-90) REVERT: B 384 VAL cc_start: 0.8082 (t) cc_final: 0.7756 (m) REVERT: B 397 GLN cc_start: 0.6821 (mm-40) cc_final: 0.6442 (mt0) REVERT: B 449 GLU cc_start: 0.6320 (mm-30) cc_final: 0.5759 (mp0) REVERT: B 477 GLN cc_start: 0.6449 (pm20) cc_final: 0.6102 (mp10) REVERT: B 480 GLU cc_start: 0.6647 (mp0) cc_final: 0.5812 (mt-10) REVERT: B 481 ARG cc_start: 0.6914 (mmm-85) cc_final: 0.6331 (ttt-90) REVERT: B 547 ARG cc_start: 0.5799 (mmm-85) cc_final: 0.5277 (mmm160) REVERT: C 97 LYS cc_start: 0.6606 (ttmm) cc_final: 0.6192 (mmmt) REVERT: C 115 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6897 (tttm) REVERT: C 125 PRO cc_start: 0.7131 (Cg_exo) cc_final: 0.6695 (Cg_endo) REVERT: C 197 ARG cc_start: 0.7361 (mtm110) cc_final: 0.6758 (mtm110) REVERT: C 198 LYS cc_start: 0.7652 (mmtp) cc_final: 0.7254 (mmmt) REVERT: C 262 MET cc_start: 0.7003 (mmm) cc_final: 0.6732 (mmm) REVERT: C 338 SER cc_start: 0.7952 (t) cc_final: 0.7588 (p) REVERT: C 416 ARG cc_start: 0.7149 (mtm110) cc_final: 0.6469 (mtm180) REVERT: C 440 ARG cc_start: 0.7145 (mtt-85) cc_final: 0.6638 (mtt-85) REVERT: C 442 ASN cc_start: 0.8370 (m-40) cc_final: 0.7764 (m110) REVERT: C 518 MET cc_start: 0.8238 (mtp) cc_final: 0.7975 (mtm) REVERT: C 547 ARG cc_start: 0.6223 (mtp85) cc_final: 0.5680 (mtp85) REVERT: C 550 ARG cc_start: 0.7033 (ttm-80) cc_final: 0.6198 (mtm110) REVERT: D 34 ASP cc_start: 0.7147 (m-30) cc_final: 0.6599 (t0) REVERT: D 52 GLU cc_start: 0.7591 (mm-30) cc_final: 0.6906 (mt-10) REVERT: D 269 GLU cc_start: 0.6390 (tt0) cc_final: 0.5812 (mt-10) REVERT: D 280 ARG cc_start: 0.6877 (mtp85) cc_final: 0.6041 (mtp-110) REVERT: D 305 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6633 (mtpp) REVERT: D 342 GLU cc_start: 0.7456 (tt0) cc_final: 0.7200 (tt0) REVERT: D 362 MET cc_start: 0.7487 (ttp) cc_final: 0.7096 (ttt) REVERT: D 376 LYS cc_start: 0.6561 (tppt) cc_final: 0.6102 (tttm) REVERT: D 405 THR cc_start: 0.6496 (p) cc_final: 0.6209 (t) REVERT: D 406 GLU cc_start: 0.5870 (tp30) cc_final: 0.5280 (pm20) REVERT: D 437 GLN cc_start: 0.7672 (tt0) cc_final: 0.7308 (tt0) REVERT: D 461 LYS cc_start: 0.7037 (tttt) cc_final: 0.6660 (tttp) REVERT: D 463 TYR cc_start: 0.7793 (t80) cc_final: 0.7120 (t80) REVERT: E 88 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7156 (mtt) REVERT: E 132 GLN cc_start: 0.7485 (tt0) cc_final: 0.7282 (tt0) REVERT: E 200 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6141 (mt-10) REVERT: E 209 GLU cc_start: 0.6043 (mt-10) cc_final: 0.5584 (mm-30) REVERT: E 228 THR cc_start: 0.8369 (t) cc_final: 0.7808 (m) REVERT: E 278 PRO cc_start: 0.8079 (Cg_endo) cc_final: 0.7741 (Cg_exo) REVERT: E 302 GLU cc_start: 0.6951 (tt0) cc_final: 0.5745 (tp30) REVERT: E 305 LYS cc_start: 0.7918 (mtmm) cc_final: 0.7567 (mtpp) REVERT: E 360 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6752 (mtt-85) REVERT: E 394 LYS cc_start: 0.5735 (tppt) cc_final: 0.5475 (mmtt) REVERT: E 445 MET cc_start: 0.7230 (mtp) cc_final: 0.6670 (mtt) REVERT: E 448 GLN cc_start: 0.5685 (OUTLIER) cc_final: 0.4949 (mm110) REVERT: F 7 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6837 (mt-10) REVERT: F 37 ASP cc_start: 0.7748 (p0) cc_final: 0.7512 (p0) REVERT: F 53 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6461 (pt0) REVERT: F 77 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6827 (pt0) REVERT: F 86 LYS cc_start: 0.7606 (tptp) cc_final: 0.7165 (tttt) REVERT: F 98 LYS cc_start: 0.7132 (mttt) cc_final: 0.6895 (mmtm) REVERT: F 130 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7967 (t80) REVERT: F 209 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6727 (mt-10) REVERT: F 280 ARG cc_start: 0.7532 (mtp85) cc_final: 0.7212 (mtt-85) REVERT: F 302 GLU cc_start: 0.7429 (tt0) cc_final: 0.7126 (tt0) REVERT: F 452 LYS cc_start: 0.6859 (mmtp) cc_final: 0.6647 (mmtp) REVERT: G 9 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.6347 (ptm) REVERT: G 47 MET cc_start: 0.5222 (mmm) cc_final: 0.4901 (ttm) REVERT: G 59 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.4318 (tp30) REVERT: G 181 GLN cc_start: 0.6675 (mm-40) cc_final: 0.6459 (mm-40) REVERT: H 63 MET cc_start: 0.3595 (mmm) cc_final: 0.2279 (ttp) REVERT: H 77 LEU cc_start: 0.4218 (mm) cc_final: 0.3836 (mp) REVERT: J 65 GLU cc_start: 0.4386 (mt-10) cc_final: 0.3917 (tt0) REVERT: J 86 ARG cc_start: 0.4331 (mmp80) cc_final: 0.3476 (ttm-80) REVERT: J 173 ARG cc_start: 0.3979 (mtp180) cc_final: 0.3745 (mtp85) REVERT: K 102 LYS cc_start: 0.5181 (tptp) cc_final: 0.3741 (mmtt) REVERT: L 102 GLU cc_start: 0.5619 (mp0) cc_final: 0.4521 (tp30) REVERT: L 138 ARG cc_start: 0.4481 (mtt180) cc_final: 0.3868 (mtt90) REVERT: L 153 ARG cc_start: 0.3928 (ttm170) cc_final: 0.3335 (ttm-80) outliers start: 92 outliers final: 64 residues processed: 529 average time/residue: 0.5173 time to fit residues: 403.5284 Evaluate side-chains 504 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 429 time to evaluate : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain J residue 105 ARG Chi-restraints excluded: chain L residue 164 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 7.9990 chunk 255 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 227 optimal weight: 5.9990 chunk 340 optimal weight: 8.9990 chunk 360 optimal weight: 0.8980 chunk 177 optimal weight: 8.9990 chunk 322 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 HIS B 290 ASN B 316 GLN C 316 GLN C 397 GLN D 364 ASN E 363 ASN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 ASN G 180 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 30052 Z= 0.322 Angle : 0.582 8.064 40716 Z= 0.303 Chirality : 0.046 0.223 4564 Planarity : 0.006 0.047 5331 Dihedral : 5.438 69.927 4214 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.58 % Favored : 97.40 % Rotamer: Outliers : 2.72 % Allowed : 13.72 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3764 helix: 0.59 (0.13), residues: 1554 sheet: -0.82 (0.20), residues: 595 loop : -0.24 (0.16), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 119 HIS 0.008 0.001 HIS D 375 PHE 0.020 0.002 PHE C 230 TYR 0.013 0.002 TYR D 283 ARG 0.010 0.001 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 430 time to evaluate : 3.739 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: A 62 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7289 (mt-10) REVERT: A 93 ARG cc_start: 0.7097 (mmm160) cc_final: 0.6773 (mpt180) REVERT: A 95 ARG cc_start: 0.6496 (tpt-90) cc_final: 0.5794 (tpt-90) REVERT: A 119 TRP cc_start: 0.8215 (OUTLIER) cc_final: 0.6947 (t-100) REVERT: A 152 ASP cc_start: 0.7383 (p0) cc_final: 0.7147 (m-30) REVERT: A 154 ARG cc_start: 0.7051 (mtp85) cc_final: 0.6728 (mtp180) REVERT: A 156 ARG cc_start: 0.6033 (mtp-110) cc_final: 0.5099 (ttp-170) REVERT: A 169 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6769 (mm-30) REVERT: A 174 VAL cc_start: 0.7630 (t) cc_final: 0.7290 (p) REVERT: A 257 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7452 (mm-30) REVERT: A 332 GLU cc_start: 0.6573 (mt-10) cc_final: 0.6178 (mt-10) REVERT: A 374 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6079 (tt0) REVERT: A 416 ARG cc_start: 0.7426 (mtm-85) cc_final: 0.6356 (mtp85) REVERT: A 478 ASP cc_start: 0.6455 (m-30) cc_final: 0.6037 (m-30) REVERT: A 481 ARG cc_start: 0.7204 (mtm-85) cc_final: 0.6525 (mtp-110) REVERT: A 517 LYS cc_start: 0.6945 (mmtp) cc_final: 0.6687 (mtpt) REVERT: A 518 MET cc_start: 0.8331 (mtp) cc_final: 0.7985 (mtm) REVERT: A 541 GLN cc_start: 0.6309 (mt0) cc_final: 0.5828 (pt0) REVERT: A 546 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6115 (mm-30) REVERT: A 550 ARG cc_start: 0.7010 (mtm-85) cc_final: 0.6569 (tpp-160) REVERT: A 557 GLU cc_start: 0.7286 (pm20) cc_final: 0.6548 (tp30) REVERT: B 119 TRP cc_start: 0.6975 (t60) cc_final: 0.6751 (t60) REVERT: B 128 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6157 (tm-30) REVERT: B 134 VAL cc_start: 0.7455 (m) cc_final: 0.7188 (t) REVERT: B 154 ARG cc_start: 0.6618 (ptp90) cc_final: 0.6367 (ptp90) REVERT: B 166 TYR cc_start: 0.7147 (m-80) cc_final: 0.6053 (m-80) REVERT: B 197 ARG cc_start: 0.6657 (ttp80) cc_final: 0.6189 (ttp-110) REVERT: B 211 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7778 (tt) REVERT: B 241 LEU cc_start: 0.7638 (mp) cc_final: 0.7375 (tt) REVERT: B 340 ARG cc_start: 0.6823 (tpp-160) cc_final: 0.6522 (tpt-90) REVERT: B 384 VAL cc_start: 0.8008 (t) cc_final: 0.7669 (m) REVERT: B 397 GLN cc_start: 0.6867 (mm-40) cc_final: 0.6419 (tt0) REVERT: B 449 GLU cc_start: 0.6209 (mm-30) cc_final: 0.5713 (mp0) REVERT: B 477 GLN cc_start: 0.6440 (pm20) cc_final: 0.6145 (mp10) REVERT: B 480 GLU cc_start: 0.6680 (mp0) cc_final: 0.5877 (mt-10) REVERT: B 481 ARG cc_start: 0.6957 (mmm-85) cc_final: 0.6370 (ttt-90) REVERT: B 547 ARG cc_start: 0.5716 (mmm-85) cc_final: 0.5206 (mmm160) REVERT: C 3 GLN cc_start: 0.7192 (mt0) cc_final: 0.6901 (mt0) REVERT: C 122 MET cc_start: 0.7383 (mtm) cc_final: 0.7125 (mtp) REVERT: C 125 PRO cc_start: 0.7116 (Cg_exo) cc_final: 0.6675 (Cg_endo) REVERT: C 198 LYS cc_start: 0.7657 (mmtp) cc_final: 0.7294 (mmmt) REVERT: C 262 MET cc_start: 0.6864 (mmm) cc_final: 0.6661 (mmm) REVERT: C 338 SER cc_start: 0.7885 (t) cc_final: 0.7605 (p) REVERT: C 416 ARG cc_start: 0.7143 (mtm110) cc_final: 0.6468 (mtm180) REVERT: C 442 ASN cc_start: 0.8374 (m-40) cc_final: 0.7754 (m110) REVERT: C 454 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7180 (mt) REVERT: C 460 ARG cc_start: 0.7022 (mtp180) cc_final: 0.6765 (mtm-85) REVERT: C 518 MET cc_start: 0.8140 (mtp) cc_final: 0.7861 (mtm) REVERT: C 547 ARG cc_start: 0.6170 (mtp85) cc_final: 0.5590 (mtp85) REVERT: C 550 ARG cc_start: 0.7002 (ttm-80) cc_final: 0.6133 (mtm110) REVERT: D 52 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6745 (mt-10) REVERT: D 269 GLU cc_start: 0.6250 (tt0) cc_final: 0.5676 (mt-10) REVERT: D 280 ARG cc_start: 0.6820 (mtp85) cc_final: 0.6201 (mtp-110) REVERT: D 305 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6199 (mtpt) REVERT: D 321 ARG cc_start: 0.7518 (tpp80) cc_final: 0.7251 (tpp80) REVERT: D 338 GLN cc_start: 0.8559 (tt0) cc_final: 0.8025 (tp40) REVERT: D 362 MET cc_start: 0.7510 (ttp) cc_final: 0.7077 (ttt) REVERT: D 406 GLU cc_start: 0.5822 (tp30) cc_final: 0.5178 (pm20) REVERT: D 437 GLN cc_start: 0.7656 (tt0) cc_final: 0.7293 (tt0) REVERT: D 463 TYR cc_start: 0.7756 (t80) cc_final: 0.6803 (t80) REVERT: E 88 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7268 (mtt) REVERT: E 209 GLU cc_start: 0.5968 (mt-10) cc_final: 0.5464 (mm-30) REVERT: E 228 THR cc_start: 0.8353 (t) cc_final: 0.7807 (m) REVERT: E 278 PRO cc_start: 0.8087 (Cg_endo) cc_final: 0.7716 (Cg_exo) REVERT: E 302 GLU cc_start: 0.6957 (tt0) cc_final: 0.5771 (tp30) REVERT: E 305 LYS cc_start: 0.7873 (mtmm) cc_final: 0.7552 (mtpp) REVERT: E 360 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6647 (mtt-85) REVERT: E 420 ARG cc_start: 0.7629 (mtm110) cc_final: 0.7153 (mtm-85) REVERT: E 445 MET cc_start: 0.7338 (mtp) cc_final: 0.6826 (mtt) REVERT: E 448 GLN cc_start: 0.5604 (OUTLIER) cc_final: 0.5274 (mm110) REVERT: F 7 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6853 (mt-10) REVERT: F 53 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6369 (pt0) REVERT: F 77 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6841 (pt0) REVERT: F 86 LYS cc_start: 0.7492 (tptp) cc_final: 0.7038 (tttt) REVERT: F 98 LYS cc_start: 0.7052 (mttt) cc_final: 0.6819 (mmtm) REVERT: F 207 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6142 (tm-30) REVERT: F 209 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6734 (mt-10) REVERT: F 210 ARG cc_start: 0.5949 (ttp80) cc_final: 0.5493 (ttp80) REVERT: F 280 ARG cc_start: 0.7456 (mtp85) cc_final: 0.7192 (mtt180) REVERT: F 302 GLU cc_start: 0.7418 (tt0) cc_final: 0.7015 (tt0) REVERT: F 362 MET cc_start: 0.8344 (ttm) cc_final: 0.7995 (ttt) REVERT: F 452 LYS cc_start: 0.6898 (mmtp) cc_final: 0.6646 (mmtp) REVERT: G 9 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.6326 (ptm) REVERT: G 47 MET cc_start: 0.5418 (mmm) cc_final: 0.4898 (ttm) REVERT: G 59 GLU cc_start: 0.5486 (OUTLIER) cc_final: 0.4284 (tp30) REVERT: G 181 GLN cc_start: 0.6606 (mm-40) cc_final: 0.6378 (mm-40) REVERT: G 200 LYS cc_start: 0.5091 (OUTLIER) cc_final: 0.4751 (mttt) REVERT: H 63 MET cc_start: 0.3405 (mmm) cc_final: 0.2122 (ttp) REVERT: H 77 LEU cc_start: 0.4085 (mm) cc_final: 0.3650 (mt) REVERT: J 65 GLU cc_start: 0.4429 (mt-10) cc_final: 0.4001 (tt0) REVERT: J 86 ARG cc_start: 0.4306 (mmp80) cc_final: 0.3457 (ttm-80) REVERT: J 173 ARG cc_start: 0.3950 (mtp180) cc_final: 0.3715 (mtp85) REVERT: K 102 LYS cc_start: 0.5025 (tptp) cc_final: 0.3710 (mmtt) REVERT: L 102 GLU cc_start: 0.5483 (mp0) cc_final: 0.4448 (tp30) REVERT: L 138 ARG cc_start: 0.4509 (mtt180) cc_final: 0.3898 (mtt90) REVERT: L 153 ARG cc_start: 0.4013 (ttm170) cc_final: 0.3433 (ttm-80) outliers start: 84 outliers final: 51 residues processed: 485 average time/residue: 0.5287 time to fit residues: 379.7890 Evaluate side-chains 483 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 421 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 200 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 7.9990 chunk 204 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 268 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 249 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 323 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS A 498 ASN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN F 413 GLN G 180 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 30052 Z= 0.279 Angle : 0.549 7.650 40716 Z= 0.285 Chirality : 0.045 0.212 4564 Planarity : 0.005 0.047 5331 Dihedral : 5.286 68.486 4214 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.02 % Rotamer: Outliers : 3.15 % Allowed : 14.17 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3764 helix: 0.70 (0.14), residues: 1537 sheet: -0.75 (0.20), residues: 589 loop : -0.20 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 119 HIS 0.007 0.001 HIS D 375 PHE 0.019 0.002 PHE C 230 TYR 0.015 0.001 TYR F 203 ARG 0.010 0.001 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 421 time to evaluate : 4.127 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: A 95 ARG cc_start: 0.6454 (tpt-90) cc_final: 0.5883 (tpt-90) REVERT: A 152 ASP cc_start: 0.7418 (p0) cc_final: 0.7204 (m-30) REVERT: A 154 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6795 (mtp180) REVERT: A 156 ARG cc_start: 0.6059 (mtp-110) cc_final: 0.5125 (ttp-170) REVERT: A 169 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6712 (mm-30) REVERT: A 174 VAL cc_start: 0.7638 (t) cc_final: 0.7313 (p) REVERT: A 257 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 332 GLU cc_start: 0.6600 (mt-10) cc_final: 0.6143 (mt-10) REVERT: A 374 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6086 (tt0) REVERT: A 416 ARG cc_start: 0.7414 (mtm-85) cc_final: 0.6306 (mtp85) REVERT: A 478 ASP cc_start: 0.6450 (m-30) cc_final: 0.6162 (m-30) REVERT: A 481 ARG cc_start: 0.7200 (mtm-85) cc_final: 0.6522 (mtp-110) REVERT: A 517 LYS cc_start: 0.6912 (mmtp) cc_final: 0.6662 (mtpt) REVERT: A 518 MET cc_start: 0.8291 (mtp) cc_final: 0.7969 (mtm) REVERT: A 541 GLN cc_start: 0.6363 (mt0) cc_final: 0.5757 (pt0) REVERT: A 550 ARG cc_start: 0.6962 (mtm-85) cc_final: 0.6531 (tpp-160) REVERT: A 557 GLU cc_start: 0.7211 (pm20) cc_final: 0.6497 (tp30) REVERT: B 128 GLU cc_start: 0.6669 (mm-30) cc_final: 0.6006 (tm-30) REVERT: B 129 VAL cc_start: 0.7672 (OUTLIER) cc_final: 0.7087 (m) REVERT: B 134 VAL cc_start: 0.7450 (m) cc_final: 0.7202 (t) REVERT: B 154 ARG cc_start: 0.6515 (ptp90) cc_final: 0.6090 (ptp90) REVERT: B 166 TYR cc_start: 0.7124 (m-80) cc_final: 0.6118 (m-80) REVERT: B 197 ARG cc_start: 0.6635 (ttp80) cc_final: 0.6177 (ttp-110) REVERT: B 211 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7814 (tt) REVERT: B 241 LEU cc_start: 0.7621 (mp) cc_final: 0.7356 (tt) REVERT: B 273 THR cc_start: 0.7854 (p) cc_final: 0.7648 (t) REVERT: B 340 ARG cc_start: 0.6815 (tpp-160) cc_final: 0.6501 (tpt-90) REVERT: B 384 VAL cc_start: 0.7960 (t) cc_final: 0.7639 (m) REVERT: B 397 GLN cc_start: 0.6840 (mm-40) cc_final: 0.6356 (tt0) REVERT: B 449 GLU cc_start: 0.6175 (mm-30) cc_final: 0.5695 (mp0) REVERT: B 477 GLN cc_start: 0.6594 (pm20) cc_final: 0.6111 (mp10) REVERT: B 480 GLU cc_start: 0.6737 (mp0) cc_final: 0.5879 (mt-10) REVERT: B 481 ARG cc_start: 0.6916 (mmm-85) cc_final: 0.6350 (ttt-90) REVERT: B 547 ARG cc_start: 0.5702 (mmm-85) cc_final: 0.5071 (ttm-80) REVERT: C 3 GLN cc_start: 0.7172 (mt0) cc_final: 0.6868 (mt0) REVERT: C 115 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6972 (tttm) REVERT: C 122 MET cc_start: 0.7417 (mtm) cc_final: 0.7147 (mtp) REVERT: C 125 PRO cc_start: 0.7098 (Cg_exo) cc_final: 0.6690 (Cg_endo) REVERT: C 198 LYS cc_start: 0.7665 (mmtp) cc_final: 0.7335 (mmmt) REVERT: C 338 SER cc_start: 0.7901 (t) cc_final: 0.7602 (p) REVERT: C 344 MET cc_start: 0.7863 (mmt) cc_final: 0.6955 (mmm) REVERT: C 416 ARG cc_start: 0.7190 (mtm110) cc_final: 0.6527 (mtm180) REVERT: C 442 ASN cc_start: 0.8392 (m-40) cc_final: 0.7769 (m110) REVERT: C 460 ARG cc_start: 0.6955 (mtp180) cc_final: 0.6704 (mtm-85) REVERT: C 547 ARG cc_start: 0.6205 (mtp85) cc_final: 0.5803 (mtp180) REVERT: C 550 ARG cc_start: 0.7080 (ttm-80) cc_final: 0.6306 (mtm110) REVERT: C 552 ARG cc_start: 0.8132 (ptt90) cc_final: 0.7845 (ptt180) REVERT: D 34 ASP cc_start: 0.7076 (m-30) cc_final: 0.6549 (t0) REVERT: D 52 GLU cc_start: 0.7496 (mm-30) cc_final: 0.6796 (mt-10) REVERT: D 269 GLU cc_start: 0.6170 (tt0) cc_final: 0.5617 (mt-10) REVERT: D 305 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6211 (mtpt) REVERT: D 362 MET cc_start: 0.7513 (ttp) cc_final: 0.7042 (ttt) REVERT: D 406 GLU cc_start: 0.5804 (tp30) cc_final: 0.5206 (pm20) REVERT: D 437 GLN cc_start: 0.7654 (tt0) cc_final: 0.7346 (tt0) REVERT: D 444 SER cc_start: 0.7424 (p) cc_final: 0.7104 (m) REVERT: D 446 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7274 (mt) REVERT: D 463 TYR cc_start: 0.7761 (t80) cc_final: 0.6858 (t80) REVERT: E 88 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7277 (mtt) REVERT: E 141 MET cc_start: 0.7787 (mtp) cc_final: 0.7405 (mmm) REVERT: E 209 GLU cc_start: 0.5912 (mt-10) cc_final: 0.5504 (mm-30) REVERT: E 228 THR cc_start: 0.8364 (t) cc_final: 0.7819 (m) REVERT: E 248 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6762 (mt-10) REVERT: E 259 ASP cc_start: 0.6459 (m-30) cc_final: 0.5970 (m-30) REVERT: E 302 GLU cc_start: 0.6848 (tt0) cc_final: 0.5664 (tp30) REVERT: E 305 LYS cc_start: 0.7883 (mtmm) cc_final: 0.7561 (mtpp) REVERT: E 360 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6678 (mtt-85) REVERT: E 410 ARG cc_start: 0.5511 (mtm-85) cc_final: 0.4207 (mmp80) REVERT: E 445 MET cc_start: 0.7374 (mtp) cc_final: 0.6870 (mtt) REVERT: F 7 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6569 (mt-10) REVERT: F 53 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6344 (pt0) REVERT: F 77 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6801 (pt0) REVERT: F 86 LYS cc_start: 0.7426 (tptp) cc_final: 0.6954 (tttt) REVERT: F 98 LYS cc_start: 0.7129 (mttt) cc_final: 0.6898 (mmtm) REVERT: F 130 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7497 (t80) REVERT: F 207 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6139 (tm-30) REVERT: F 209 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6812 (mt-10) REVERT: F 210 ARG cc_start: 0.5951 (ttp80) cc_final: 0.5694 (ttp80) REVERT: F 280 ARG cc_start: 0.7411 (mtp85) cc_final: 0.7162 (mtt180) REVERT: F 302 GLU cc_start: 0.7366 (tt0) cc_final: 0.6972 (tt0) REVERT: F 362 MET cc_start: 0.8373 (ttm) cc_final: 0.8034 (ttt) REVERT: F 452 LYS cc_start: 0.6933 (mmtp) cc_final: 0.6512 (mmtp) REVERT: G 9 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6348 (ptm) REVERT: G 47 MET cc_start: 0.5302 (mmm) cc_final: 0.4809 (ttm) REVERT: G 59 GLU cc_start: 0.5564 (OUTLIER) cc_final: 0.4363 (tp30) REVERT: G 149 LYS cc_start: 0.7411 (tptt) cc_final: 0.7134 (tptt) REVERT: G 181 GLN cc_start: 0.6659 (mm-40) cc_final: 0.6425 (mm-40) REVERT: G 200 LYS cc_start: 0.5116 (OUTLIER) cc_final: 0.4702 (mttt) REVERT: H 63 MET cc_start: 0.3462 (mmm) cc_final: 0.2004 (ttp) REVERT: H 77 LEU cc_start: 0.4154 (mm) cc_final: 0.3621 (mt) REVERT: J 65 GLU cc_start: 0.4352 (mt-10) cc_final: 0.3946 (mt-10) REVERT: J 86 ARG cc_start: 0.4310 (mmp80) cc_final: 0.3438 (ttm-80) REVERT: J 112 LEU cc_start: 0.4361 (mp) cc_final: 0.4111 (mp) REVERT: J 126 GLU cc_start: 0.1778 (OUTLIER) cc_final: 0.1007 (mp0) REVERT: J 184 GLN cc_start: 0.3640 (OUTLIER) cc_final: 0.2915 (tm-30) REVERT: K 102 LYS cc_start: 0.5126 (tptp) cc_final: 0.3787 (mmtt) REVERT: L 102 GLU cc_start: 0.5475 (mp0) cc_final: 0.4451 (tp30) REVERT: L 164 GLU cc_start: 0.5739 (tp30) cc_final: 0.4895 (mt-10) outliers start: 97 outliers final: 67 residues processed: 488 average time/residue: 0.5253 time to fit residues: 379.9068 Evaluate side-chains 493 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 412 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 413 GLN Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain J residue 126 GLU Chi-restraints excluded: chain J residue 184 GLN Chi-restraints excluded: chain L residue 107 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 6.9990 chunk 324 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 360 optimal weight: 5.9990 chunk 299 optimal weight: 0.0770 chunk 167 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 189 optimal weight: 9.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 377 GLN E 427 GLN F 388 ASN G 162 ASN G 180 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 30052 Z= 0.419 Angle : 0.646 10.701 40716 Z= 0.336 Chirality : 0.048 0.238 4564 Planarity : 0.006 0.049 5331 Dihedral : 5.670 71.172 4214 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 4.18 % Allowed : 13.88 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3764 helix: 0.38 (0.13), residues: 1543 sheet: -0.81 (0.20), residues: 601 loop : -0.35 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 175 HIS 0.009 0.001 HIS D 375 PHE 0.018 0.002 PHE F 414 TYR 0.016 0.002 TYR D 283 ARG 0.012 0.001 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 418 time to evaluate : 3.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: A 53 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: A 95 ARG cc_start: 0.6488 (tpt-90) cc_final: 0.5861 (tpt-90) REVERT: A 119 TRP cc_start: 0.8222 (OUTLIER) cc_final: 0.7111 (t-100) REVERT: A 152 ASP cc_start: 0.7422 (p0) cc_final: 0.7203 (m-30) REVERT: A 154 ARG cc_start: 0.7072 (mtp85) cc_final: 0.6764 (mtp180) REVERT: A 169 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7065 (mm-30) REVERT: A 174 VAL cc_start: 0.7652 (t) cc_final: 0.7315 (p) REVERT: A 257 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7500 (mm-30) REVERT: A 374 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6075 (tt0) REVERT: A 416 ARG cc_start: 0.7526 (mtm-85) cc_final: 0.6385 (mtp85) REVERT: A 478 ASP cc_start: 0.6431 (m-30) cc_final: 0.6017 (m-30) REVERT: A 481 ARG cc_start: 0.7246 (mtm-85) cc_final: 0.6514 (mmm160) REVERT: A 518 MET cc_start: 0.8271 (mtp) cc_final: 0.7920 (mtm) REVERT: A 541 GLN cc_start: 0.6280 (mt0) cc_final: 0.5549 (pt0) REVERT: A 550 ARG cc_start: 0.7009 (mtm-85) cc_final: 0.6590 (tpp-160) REVERT: A 557 GLU cc_start: 0.7255 (pm20) cc_final: 0.6459 (tp30) REVERT: B 29 LYS cc_start: 0.7224 (mtpt) cc_final: 0.6869 (mttt) REVERT: B 128 GLU cc_start: 0.6621 (mm-30) cc_final: 0.5991 (tm-30) REVERT: B 129 VAL cc_start: 0.7761 (OUTLIER) cc_final: 0.7169 (m) REVERT: B 134 VAL cc_start: 0.7417 (OUTLIER) cc_final: 0.7138 (t) REVERT: B 154 ARG cc_start: 0.6618 (ptp90) cc_final: 0.6147 (ptt-90) REVERT: B 180 GLU cc_start: 0.6862 (tt0) cc_final: 0.6314 (tt0) REVERT: B 197 ARG cc_start: 0.6646 (ttp80) cc_final: 0.6181 (ttp-110) REVERT: B 211 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7861 (tt) REVERT: B 241 LEU cc_start: 0.7643 (mp) cc_final: 0.7362 (tt) REVERT: B 273 THR cc_start: 0.7817 (p) cc_final: 0.7610 (t) REVERT: B 323 MET cc_start: 0.8870 (mtp) cc_final: 0.8581 (mtm) REVERT: B 340 ARG cc_start: 0.6894 (tpp-160) cc_final: 0.6580 (tpt-90) REVERT: B 384 VAL cc_start: 0.8016 (t) cc_final: 0.7682 (m) REVERT: B 397 GLN cc_start: 0.6815 (mm-40) cc_final: 0.6386 (tt0) REVERT: B 449 GLU cc_start: 0.6205 (mm-30) cc_final: 0.5735 (mp0) REVERT: B 480 GLU cc_start: 0.6693 (mp0) cc_final: 0.5772 (mt-10) REVERT: B 481 ARG cc_start: 0.6961 (mmm-85) cc_final: 0.6375 (ttt-90) REVERT: B 493 ASP cc_start: 0.6959 (m-30) cc_final: 0.6527 (m-30) REVERT: B 527 GLU cc_start: 0.5783 (OUTLIER) cc_final: 0.5263 (tt0) REVERT: B 547 ARG cc_start: 0.5745 (mmm-85) cc_final: 0.5097 (ttm-80) REVERT: C 3 GLN cc_start: 0.7236 (mt0) cc_final: 0.6922 (mt0) REVERT: C 97 LYS cc_start: 0.6645 (ttmm) cc_final: 0.5744 (mptt) REVERT: C 115 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6878 (tttm) REVERT: C 122 MET cc_start: 0.7471 (mtm) cc_final: 0.7184 (mtp) REVERT: C 125 PRO cc_start: 0.7151 (Cg_exo) cc_final: 0.6690 (Cg_endo) REVERT: C 338 SER cc_start: 0.8002 (t) cc_final: 0.7682 (p) REVERT: C 344 MET cc_start: 0.7873 (mmt) cc_final: 0.6906 (mmm) REVERT: C 416 ARG cc_start: 0.7147 (mtm110) cc_final: 0.6471 (mtm180) REVERT: C 442 ASN cc_start: 0.8379 (m-40) cc_final: 0.8067 (m-40) REVERT: C 445 GLU cc_start: 0.6600 (mm-30) cc_final: 0.6131 (tt0) REVERT: C 460 ARG cc_start: 0.7031 (mtp180) cc_final: 0.6782 (mtm-85) REVERT: C 547 ARG cc_start: 0.6410 (mtp85) cc_final: 0.5721 (mtp85) REVERT: C 550 ARG cc_start: 0.7030 (ttm-80) cc_final: 0.6214 (mtm110) REVERT: C 552 ARG cc_start: 0.8102 (ptt90) cc_final: 0.7884 (ptt180) REVERT: D 26 ASP cc_start: 0.7621 (t0) cc_final: 0.7333 (t0) REVERT: D 52 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7331 (mm-30) REVERT: D 269 GLU cc_start: 0.6237 (tt0) cc_final: 0.5630 (mt-10) REVERT: D 280 ARG cc_start: 0.6707 (mtp85) cc_final: 0.6138 (mtp-110) REVERT: D 305 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6550 (mtpp) REVERT: D 362 MET cc_start: 0.7541 (ttp) cc_final: 0.7056 (ttt) REVERT: D 406 GLU cc_start: 0.5906 (tp30) cc_final: 0.5331 (pm20) REVERT: D 437 GLN cc_start: 0.7760 (tt0) cc_final: 0.7453 (tt0) REVERT: D 444 SER cc_start: 0.7681 (p) cc_final: 0.7230 (m) REVERT: D 463 TYR cc_start: 0.7768 (t80) cc_final: 0.6790 (t80) REVERT: E 88 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7225 (mtt) REVERT: E 132 GLN cc_start: 0.7400 (tt0) cc_final: 0.7166 (tt0) REVERT: E 228 THR cc_start: 0.8466 (t) cc_final: 0.7898 (m) REVERT: E 302 GLU cc_start: 0.6993 (tt0) cc_final: 0.5792 (tp30) REVERT: E 305 LYS cc_start: 0.7923 (mtmm) cc_final: 0.7631 (mtpp) REVERT: E 360 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6744 (mtt-85) REVERT: E 368 LYS cc_start: 0.6164 (OUTLIER) cc_final: 0.5707 (tppt) REVERT: E 410 ARG cc_start: 0.5563 (mtm-85) cc_final: 0.4322 (mmp80) REVERT: F 53 GLU cc_start: 0.6676 (mt-10) cc_final: 0.6215 (pt0) REVERT: F 77 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6714 (pt0) REVERT: F 86 LYS cc_start: 0.7474 (tptp) cc_final: 0.7266 (tttt) REVERT: F 98 LYS cc_start: 0.7044 (mttt) cc_final: 0.6799 (mmtm) REVERT: F 109 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6354 (mm-30) REVERT: F 130 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7646 (t80) REVERT: F 207 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6186 (tm-30) REVERT: F 209 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6841 (mt-10) REVERT: F 210 ARG cc_start: 0.5902 (ttp80) cc_final: 0.5527 (ttp80) REVERT: F 280 ARG cc_start: 0.7449 (mtp85) cc_final: 0.7209 (mtt180) REVERT: F 302 GLU cc_start: 0.7407 (tt0) cc_final: 0.6947 (tt0) REVERT: F 362 MET cc_start: 0.8371 (ttm) cc_final: 0.8038 (ttt) REVERT: F 452 LYS cc_start: 0.6987 (mmtp) cc_final: 0.6522 (mmtp) REVERT: G 9 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.6396 (ptm) REVERT: G 47 MET cc_start: 0.5252 (mmm) cc_final: 0.4746 (ttm) REVERT: G 59 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.4387 (tp30) REVERT: G 181 GLN cc_start: 0.6555 (mm-40) cc_final: 0.6345 (mm-40) REVERT: G 200 LYS cc_start: 0.5042 (OUTLIER) cc_final: 0.4748 (mttt) REVERT: H 63 MET cc_start: 0.3184 (mmm) cc_final: 0.2812 (tpp) REVERT: H 77 LEU cc_start: 0.4312 (mm) cc_final: 0.3763 (mt) REVERT: J 65 GLU cc_start: 0.4196 (mt-10) cc_final: 0.3741 (tt0) REVERT: J 86 ARG cc_start: 0.4331 (mmp80) cc_final: 0.3423 (ttm-80) REVERT: J 112 LEU cc_start: 0.4546 (OUTLIER) cc_final: 0.4252 (mp) REVERT: J 126 GLU cc_start: 0.1831 (OUTLIER) cc_final: 0.1274 (mp0) REVERT: J 184 GLN cc_start: 0.3722 (OUTLIER) cc_final: 0.2963 (tm-30) REVERT: K 102 LYS cc_start: 0.5182 (tptp) cc_final: 0.3830 (mmtt) REVERT: L 102 GLU cc_start: 0.5559 (mp0) cc_final: 0.4487 (tp30) REVERT: L 164 GLU cc_start: 0.5575 (tp30) cc_final: 0.5041 (mt-10) outliers start: 129 outliers final: 88 residues processed: 512 average time/residue: 0.5019 time to fit residues: 379.7490 Evaluate side-chains 524 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 417 time to evaluate : 4.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 126 GLU Chi-restraints excluded: chain J residue 184 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 263 optimal weight: 8.9990 chunk 204 optimal weight: 0.8980 chunk 303 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 359 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 238 GLN E 161 ASN F 388 ASN F 413 GLN G 180 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30052 Z= 0.186 Angle : 0.496 6.666 40716 Z= 0.259 Chirality : 0.043 0.255 4564 Planarity : 0.005 0.049 5331 Dihedral : 5.080 67.497 4214 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.18 % Favored : 97.79 % Rotamer: Outliers : 2.85 % Allowed : 15.83 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3764 helix: 0.82 (0.14), residues: 1535 sheet: -0.70 (0.20), residues: 591 loop : -0.22 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 119 HIS 0.004 0.001 HIS D 375 PHE 0.021 0.001 PHE C 230 TYR 0.011 0.001 TYR D 463 ARG 0.007 0.000 ARG L 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 425 time to evaluate : 3.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: A 53 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6990 (mt-10) REVERT: A 95 ARG cc_start: 0.6427 (tpt-90) cc_final: 0.5842 (tpt-90) REVERT: A 119 TRP cc_start: 0.8228 (OUTLIER) cc_final: 0.7144 (t-100) REVERT: A 154 ARG cc_start: 0.7039 (mtp85) cc_final: 0.6671 (mtp180) REVERT: A 156 ARG cc_start: 0.5991 (mtp-110) cc_final: 0.5067 (ttp-170) REVERT: A 169 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6819 (mt-10) REVERT: A 174 VAL cc_start: 0.7521 (t) cc_final: 0.7200 (p) REVERT: A 257 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7384 (mm-30) REVERT: A 374 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6061 (tt0) REVERT: A 416 ARG cc_start: 0.7474 (mtm-85) cc_final: 0.6350 (mtp85) REVERT: A 478 ASP cc_start: 0.6368 (m-30) cc_final: 0.6073 (m-30) REVERT: A 481 ARG cc_start: 0.7114 (mtm-85) cc_final: 0.6435 (mtp-110) REVERT: A 518 MET cc_start: 0.8318 (mtp) cc_final: 0.8023 (mtm) REVERT: A 541 GLN cc_start: 0.6303 (mt0) cc_final: 0.5731 (pt0) REVERT: A 550 ARG cc_start: 0.6821 (mtm-85) cc_final: 0.6530 (tpp-160) REVERT: A 557 GLU cc_start: 0.7243 (pm20) cc_final: 0.6356 (tp30) REVERT: B 29 LYS cc_start: 0.7233 (mtpt) cc_final: 0.6829 (mttm) REVERT: B 128 GLU cc_start: 0.6617 (mm-30) cc_final: 0.6082 (tm-30) REVERT: B 129 VAL cc_start: 0.7595 (p) cc_final: 0.7039 (m) REVERT: B 134 VAL cc_start: 0.7408 (m) cc_final: 0.7176 (t) REVERT: B 154 ARG cc_start: 0.6515 (ptp90) cc_final: 0.6230 (ptm-80) REVERT: B 161 LYS cc_start: 0.6593 (OUTLIER) cc_final: 0.6298 (mmtm) REVERT: B 180 GLU cc_start: 0.6802 (tt0) cc_final: 0.6292 (tt0) REVERT: B 197 ARG cc_start: 0.6557 (ttp80) cc_final: 0.6106 (ttp-110) REVERT: B 273 THR cc_start: 0.7846 (p) cc_final: 0.7641 (t) REVERT: B 282 MET cc_start: 0.8178 (tpt) cc_final: 0.7945 (tpt) REVERT: B 340 ARG cc_start: 0.6765 (tpp-160) cc_final: 0.6444 (tpt-90) REVERT: B 384 VAL cc_start: 0.7902 (t) cc_final: 0.7577 (m) REVERT: B 397 GLN cc_start: 0.6790 (mm-40) cc_final: 0.6324 (tt0) REVERT: B 449 GLU cc_start: 0.6176 (mm-30) cc_final: 0.5441 (mt-10) REVERT: B 481 ARG cc_start: 0.6888 (mmm-85) cc_final: 0.6333 (ttt-90) REVERT: B 493 ASP cc_start: 0.6991 (m-30) cc_final: 0.6614 (m-30) REVERT: B 527 GLU cc_start: 0.5713 (OUTLIER) cc_final: 0.5291 (tt0) REVERT: B 547 ARG cc_start: 0.5624 (mmm-85) cc_final: 0.5044 (ttm-80) REVERT: C 3 GLN cc_start: 0.7189 (mt0) cc_final: 0.6914 (mt0) REVERT: C 92 GLU cc_start: 0.7392 (pm20) cc_final: 0.6930 (mt-10) REVERT: C 122 MET cc_start: 0.7504 (mtm) cc_final: 0.7213 (mtp) REVERT: C 125 PRO cc_start: 0.7076 (Cg_exo) cc_final: 0.6685 (Cg_endo) REVERT: C 197 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6850 (ptm-80) REVERT: C 338 SER cc_start: 0.7845 (t) cc_final: 0.7535 (p) REVERT: C 344 MET cc_start: 0.7782 (mmt) cc_final: 0.6994 (mmm) REVERT: C 416 ARG cc_start: 0.7171 (mtm110) cc_final: 0.6521 (mtm180) REVERT: C 442 ASN cc_start: 0.8412 (m-40) cc_final: 0.7782 (m110) REVERT: C 445 GLU cc_start: 0.6654 (mm-30) cc_final: 0.6156 (tt0) REVERT: C 547 ARG cc_start: 0.6310 (mtp85) cc_final: 0.5947 (mtp180) REVERT: C 550 ARG cc_start: 0.7014 (ttm-80) cc_final: 0.6254 (mtm110) REVERT: C 552 ARG cc_start: 0.8064 (ptt90) cc_final: 0.7812 (ptt180) REVERT: D 34 ASP cc_start: 0.6975 (m-30) cc_final: 0.6457 (t0) REVERT: D 52 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7172 (mm-30) REVERT: D 269 GLU cc_start: 0.6126 (tt0) cc_final: 0.5611 (mt-10) REVERT: D 305 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.7022 (mtpt) REVERT: D 362 MET cc_start: 0.7515 (ttp) cc_final: 0.7011 (ttt) REVERT: D 406 GLU cc_start: 0.5767 (tp30) cc_final: 0.5209 (pm20) REVERT: D 437 GLN cc_start: 0.7680 (tt0) cc_final: 0.7396 (tt0) REVERT: D 444 SER cc_start: 0.7491 (p) cc_final: 0.7120 (m) REVERT: D 446 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7283 (mt) REVERT: D 463 TYR cc_start: 0.7750 (t80) cc_final: 0.6923 (t80) REVERT: E 88 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7247 (mtt) REVERT: E 228 THR cc_start: 0.8364 (t) cc_final: 0.8012 (m) REVERT: E 259 ASP cc_start: 0.6291 (m-30) cc_final: 0.5804 (m-30) REVERT: E 302 GLU cc_start: 0.6988 (tt0) cc_final: 0.5773 (tp30) REVERT: E 305 LYS cc_start: 0.7941 (mtmm) cc_final: 0.7636 (mtpp) REVERT: E 360 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6688 (mtt-85) REVERT: E 368 LYS cc_start: 0.6101 (OUTLIER) cc_final: 0.5678 (tppt) REVERT: E 410 ARG cc_start: 0.5563 (mtm-85) cc_final: 0.4235 (mmp80) REVERT: E 445 MET cc_start: 0.7394 (mtp) cc_final: 0.6858 (mtt) REVERT: F 53 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6268 (pt0) REVERT: F 77 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6794 (pt0) REVERT: F 86 LYS cc_start: 0.7397 (tptp) cc_final: 0.7191 (tttt) REVERT: F 98 LYS cc_start: 0.7087 (mttt) cc_final: 0.6760 (mmtm) REVERT: F 109 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6281 (mm-30) REVERT: F 130 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7569 (t80) REVERT: F 207 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6169 (tm-30) REVERT: F 209 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6867 (mt-10) REVERT: F 210 ARG cc_start: 0.5924 (ttp80) cc_final: 0.4990 (mtm110) REVERT: F 280 ARG cc_start: 0.7414 (mtp85) cc_final: 0.7157 (mtt180) REVERT: F 302 GLU cc_start: 0.7429 (tt0) cc_final: 0.6966 (tt0) REVERT: F 362 MET cc_start: 0.8354 (ttm) cc_final: 0.8053 (ttt) REVERT: F 452 LYS cc_start: 0.6963 (mmtp) cc_final: 0.6514 (mmtp) REVERT: G 9 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6399 (ptm) REVERT: G 47 MET cc_start: 0.5377 (mmm) cc_final: 0.4778 (ttm) REVERT: G 59 GLU cc_start: 0.5596 (OUTLIER) cc_final: 0.4619 (tp30) REVERT: G 155 LYS cc_start: 0.6390 (mttt) cc_final: 0.6170 (mttp) REVERT: G 181 GLN cc_start: 0.6605 (mm-40) cc_final: 0.6395 (mm-40) REVERT: G 200 LYS cc_start: 0.4974 (OUTLIER) cc_final: 0.4593 (mttt) REVERT: H 63 MET cc_start: 0.3291 (mmm) cc_final: 0.1605 (ttm) REVERT: H 77 LEU cc_start: 0.4311 (mm) cc_final: 0.3798 (mt) REVERT: H 87 GLU cc_start: 0.4782 (mp0) cc_final: 0.4277 (mm-30) REVERT: J 65 GLU cc_start: 0.4270 (mt-10) cc_final: 0.3983 (mt-10) REVERT: J 86 ARG cc_start: 0.4286 (mmp80) cc_final: 0.3400 (ttm-80) REVERT: J 112 LEU cc_start: 0.4361 (OUTLIER) cc_final: 0.4154 (mp) REVERT: J 126 GLU cc_start: 0.1829 (OUTLIER) cc_final: 0.0947 (tt0) REVERT: J 173 ARG cc_start: 0.3764 (mtt90) cc_final: 0.2979 (mtp85) REVERT: J 184 GLN cc_start: 0.3689 (OUTLIER) cc_final: 0.2949 (tm-30) REVERT: K 102 LYS cc_start: 0.5212 (tptp) cc_final: 0.3820 (mmtt) REVERT: L 102 GLU cc_start: 0.5416 (mp0) cc_final: 0.4460 (tp30) REVERT: L 164 GLU cc_start: 0.5537 (tp30) cc_final: 0.5018 (mt-10) outliers start: 88 outliers final: 61 residues processed: 484 average time/residue: 0.5138 time to fit residues: 367.2311 Evaluate side-chains 489 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 410 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 413 GLN Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 126 GLU Chi-restraints excluded: chain J residue 184 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 69 optimal weight: 0.0050 chunk 228 optimal weight: 8.9990 chunk 244 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 282 optimal weight: 2.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 388 ASN F 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30052 Z= 0.285 Angle : 0.553 8.405 40716 Z= 0.287 Chirality : 0.045 0.258 4564 Planarity : 0.005 0.049 5331 Dihedral : 5.255 70.813 4214 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 3.47 % Allowed : 15.73 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3764 helix: 0.71 (0.14), residues: 1537 sheet: -0.71 (0.20), residues: 591 loop : -0.22 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 119 HIS 0.006 0.001 HIS D 375 PHE 0.023 0.002 PHE F 414 TYR 0.012 0.001 TYR D 283 ARG 0.007 0.000 ARG L 153 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 413 time to evaluate : 4.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: A 53 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7019 (mm-30) REVERT: A 95 ARG cc_start: 0.6455 (tpt-90) cc_final: 0.5817 (tpt-90) REVERT: A 154 ARG cc_start: 0.7031 (mtp85) cc_final: 0.6713 (mtp180) REVERT: A 169 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6847 (mt-10) REVERT: A 257 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7434 (mm-30) REVERT: A 374 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6054 (tt0) REVERT: A 416 ARG cc_start: 0.7556 (mtm-85) cc_final: 0.6436 (mtp85) REVERT: A 478 ASP cc_start: 0.6411 (m-30) cc_final: 0.6118 (m-30) REVERT: A 481 ARG cc_start: 0.7181 (mtm-85) cc_final: 0.6454 (mmm160) REVERT: A 518 MET cc_start: 0.8335 (mtp) cc_final: 0.8037 (mtm) REVERT: A 541 GLN cc_start: 0.6295 (mt0) cc_final: 0.5687 (pt0) REVERT: A 550 ARG cc_start: 0.6845 (mtm-85) cc_final: 0.6551 (tpp-160) REVERT: A 557 GLU cc_start: 0.7236 (pm20) cc_final: 0.6378 (tp30) REVERT: B 128 GLU cc_start: 0.6573 (mm-30) cc_final: 0.5971 (tm-30) REVERT: B 129 VAL cc_start: 0.7678 (p) cc_final: 0.7178 (m) REVERT: B 134 VAL cc_start: 0.7404 (m) cc_final: 0.7166 (t) REVERT: B 154 ARG cc_start: 0.6564 (ptp90) cc_final: 0.6188 (ptt-90) REVERT: B 161 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.6274 (mmtt) REVERT: B 180 GLU cc_start: 0.6843 (tt0) cc_final: 0.6319 (tt0) REVERT: B 197 ARG cc_start: 0.6625 (ttp80) cc_final: 0.6163 (ttp-110) REVERT: B 211 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7827 (tt) REVERT: B 273 THR cc_start: 0.7802 (p) cc_final: 0.7597 (t) REVERT: B 340 ARG cc_start: 0.6810 (tpp-160) cc_final: 0.6486 (tpt-90) REVERT: B 384 VAL cc_start: 0.7919 (t) cc_final: 0.7610 (m) REVERT: B 397 GLN cc_start: 0.6821 (mm-40) cc_final: 0.6392 (tt0) REVERT: B 449 GLU cc_start: 0.6157 (mm-30) cc_final: 0.5403 (mt-10) REVERT: B 481 ARG cc_start: 0.6958 (mmm-85) cc_final: 0.6380 (ttt-90) REVERT: B 527 GLU cc_start: 0.5737 (OUTLIER) cc_final: 0.5271 (tt0) REVERT: B 547 ARG cc_start: 0.5541 (mmm-85) cc_final: 0.4957 (ttm-80) REVERT: C 3 GLN cc_start: 0.7232 (mt0) cc_final: 0.6940 (mt0) REVERT: C 92 GLU cc_start: 0.7550 (pm20) cc_final: 0.7145 (mt-10) REVERT: C 97 LYS cc_start: 0.6638 (ttmm) cc_final: 0.6251 (mmmt) REVERT: C 122 MET cc_start: 0.7528 (mtm) cc_final: 0.7255 (mtp) REVERT: C 125 PRO cc_start: 0.7070 (Cg_exo) cc_final: 0.6621 (Cg_endo) REVERT: C 338 SER cc_start: 0.7934 (t) cc_final: 0.7587 (p) REVERT: C 344 MET cc_start: 0.7784 (mmt) cc_final: 0.7006 (mmm) REVERT: C 416 ARG cc_start: 0.7176 (mtm110) cc_final: 0.6516 (mtm180) REVERT: C 442 ASN cc_start: 0.8404 (m-40) cc_final: 0.8096 (m-40) REVERT: C 445 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6153 (tt0) REVERT: C 461 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7256 (tt0) REVERT: C 547 ARG cc_start: 0.6343 (mtp85) cc_final: 0.5932 (mtp180) REVERT: C 550 ARG cc_start: 0.7000 (ttm-80) cc_final: 0.6154 (mtm110) REVERT: C 552 ARG cc_start: 0.8056 (ptt90) cc_final: 0.7795 (ptt180) REVERT: C 562 TYR cc_start: 0.7755 (t80) cc_final: 0.7323 (t80) REVERT: D 52 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6841 (mt-10) REVERT: D 269 GLU cc_start: 0.6176 (tt0) cc_final: 0.5604 (mt-10) REVERT: D 305 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6509 (mtpp) REVERT: D 362 MET cc_start: 0.7525 (ttp) cc_final: 0.7020 (ttt) REVERT: D 406 GLU cc_start: 0.5894 (tp30) cc_final: 0.5267 (pm20) REVERT: D 437 GLN cc_start: 0.7754 (tt0) cc_final: 0.7466 (tt0) REVERT: D 444 SER cc_start: 0.7538 (p) cc_final: 0.7104 (m) REVERT: D 446 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7310 (mt) REVERT: D 461 LYS cc_start: 0.7060 (ttmm) cc_final: 0.6155 (mttt) REVERT: D 463 TYR cc_start: 0.7737 (t80) cc_final: 0.6764 (t80) REVERT: E 88 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7247 (mtt) REVERT: E 228 THR cc_start: 0.8415 (t) cc_final: 0.8063 (m) REVERT: E 259 ASP cc_start: 0.6561 (m-30) cc_final: 0.6310 (t0) REVERT: E 302 GLU cc_start: 0.7084 (tt0) cc_final: 0.6839 (tt0) REVERT: E 305 LYS cc_start: 0.7953 (mtmm) cc_final: 0.7669 (mtpp) REVERT: E 360 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6621 (mtt-85) REVERT: E 368 LYS cc_start: 0.6260 (OUTLIER) cc_final: 0.5694 (tppt) REVERT: E 410 ARG cc_start: 0.5514 (mtm-85) cc_final: 0.4225 (mmp80) REVERT: F 53 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6260 (pt0) REVERT: F 77 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6754 (pt0) REVERT: F 86 LYS cc_start: 0.7399 (tptp) cc_final: 0.6929 (tttt) REVERT: F 98 LYS cc_start: 0.7038 (mttt) cc_final: 0.6773 (mmtm) REVERT: F 130 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7631 (t80) REVERT: F 207 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6186 (tm-30) REVERT: F 209 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6880 (mt-10) REVERT: F 210 ARG cc_start: 0.5914 (ttp80) cc_final: 0.5061 (mtm110) REVERT: F 280 ARG cc_start: 0.7476 (mtp85) cc_final: 0.7221 (mtt180) REVERT: F 302 GLU cc_start: 0.7441 (tt0) cc_final: 0.6970 (tt0) REVERT: F 362 MET cc_start: 0.8379 (ttm) cc_final: 0.8058 (ttt) REVERT: F 452 LYS cc_start: 0.6969 (mmtp) cc_final: 0.6542 (mmtp) REVERT: G 9 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.6356 (ptm) REVERT: G 47 MET cc_start: 0.5193 (mmm) cc_final: 0.4629 (ttm) REVERT: G 59 GLU cc_start: 0.5676 (OUTLIER) cc_final: 0.4652 (tp30) REVERT: G 149 LYS cc_start: 0.7251 (tptt) cc_final: 0.6998 (tptt) REVERT: G 181 GLN cc_start: 0.6540 (mm-40) cc_final: 0.6323 (mm-40) REVERT: G 200 LYS cc_start: 0.5087 (OUTLIER) cc_final: 0.4687 (mttt) REVERT: H 63 MET cc_start: 0.3245 (mmm) cc_final: 0.1802 (ttp) REVERT: H 77 LEU cc_start: 0.4271 (mm) cc_final: 0.3741 (mt) REVERT: H 87 GLU cc_start: 0.4739 (mp0) cc_final: 0.4242 (mm-30) REVERT: J 86 ARG cc_start: 0.4221 (mmp80) cc_final: 0.3337 (ttm-80) REVERT: J 112 LEU cc_start: 0.4332 (OUTLIER) cc_final: 0.4109 (mp) REVERT: J 126 GLU cc_start: 0.1919 (OUTLIER) cc_final: 0.1061 (tt0) REVERT: J 184 GLN cc_start: 0.3655 (OUTLIER) cc_final: 0.2924 (tm-30) REVERT: K 102 LYS cc_start: 0.5238 (tptp) cc_final: 0.3881 (mmtt) REVERT: L 86 ARG cc_start: 0.4824 (mtt180) cc_final: 0.4553 (mtp180) REVERT: L 102 GLU cc_start: 0.5417 (mp0) cc_final: 0.4445 (tp30) REVERT: L 164 GLU cc_start: 0.5471 (tp30) cc_final: 0.4941 (mt-10) outliers start: 107 outliers final: 76 residues processed: 483 average time/residue: 0.5385 time to fit residues: 388.6758 Evaluate side-chains 502 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 408 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 413 GLN Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 126 GLU Chi-restraints excluded: chain J residue 184 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 0.0030 chunk 344 optimal weight: 9.9990 chunk 314 optimal weight: 2.9990 chunk 335 optimal weight: 20.0000 chunk 201 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 263 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 302 optimal weight: 2.9990 chunk 316 optimal weight: 8.9990 chunk 333 optimal weight: 30.0000 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 459 GLN E 161 ASN F 388 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30052 Z= 0.332 Angle : 0.587 9.196 40716 Z= 0.304 Chirality : 0.046 0.261 4564 Planarity : 0.006 0.049 5331 Dihedral : 5.414 75.434 4214 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.76 % Allowed : 15.67 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3764 helix: 0.57 (0.13), residues: 1548 sheet: -0.72 (0.20), residues: 599 loop : -0.26 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 175 HIS 0.007 0.001 HIS D 375 PHE 0.022 0.002 PHE F 414 TYR 0.013 0.002 TYR D 283 ARG 0.005 0.001 ARG L 153 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 413 time to evaluate : 3.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: A 53 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7122 (mm-30) REVERT: A 95 ARG cc_start: 0.6489 (tpt-90) cc_final: 0.5849 (tpt-90) REVERT: A 119 TRP cc_start: 0.8233 (OUTLIER) cc_final: 0.7175 (t-100) REVERT: A 154 ARG cc_start: 0.7009 (mtp85) cc_final: 0.6690 (mtp180) REVERT: A 169 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6846 (mt-10) REVERT: A 257 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7454 (mm-30) REVERT: A 340 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.5487 (mpp-170) REVERT: A 374 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6040 (tt0) REVERT: A 416 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.6416 (mtp85) REVERT: A 478 ASP cc_start: 0.6448 (m-30) cc_final: 0.6158 (m-30) REVERT: A 481 ARG cc_start: 0.7161 (mtm-85) cc_final: 0.6437 (mmm160) REVERT: A 518 MET cc_start: 0.8295 (mtp) cc_final: 0.7990 (mtm) REVERT: A 541 GLN cc_start: 0.6290 (mt0) cc_final: 0.5683 (pt0) REVERT: A 550 ARG cc_start: 0.6880 (mtm-85) cc_final: 0.6596 (tpp-160) REVERT: A 557 GLU cc_start: 0.7270 (pm20) cc_final: 0.6438 (tp30) REVERT: B 128 GLU cc_start: 0.6577 (mm-30) cc_final: 0.5976 (tm-30) REVERT: B 129 VAL cc_start: 0.7704 (p) cc_final: 0.7204 (m) REVERT: B 154 ARG cc_start: 0.6592 (ptp90) cc_final: 0.6177 (ptt-90) REVERT: B 161 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.6240 (mmtt) REVERT: B 180 GLU cc_start: 0.6851 (tt0) cc_final: 0.6339 (tt0) REVERT: B 197 ARG cc_start: 0.6643 (ttp80) cc_final: 0.6184 (ttp-110) REVERT: B 211 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7807 (tt) REVERT: B 340 ARG cc_start: 0.6883 (tpp-160) cc_final: 0.6550 (tpt-90) REVERT: B 384 VAL cc_start: 0.7922 (t) cc_final: 0.7611 (m) REVERT: B 397 GLN cc_start: 0.6815 (mm-40) cc_final: 0.6423 (tt0) REVERT: B 449 GLU cc_start: 0.6155 (mm-30) cc_final: 0.5396 (mt-10) REVERT: B 480 GLU cc_start: 0.6640 (mp0) cc_final: 0.5738 (mt-10) REVERT: B 481 ARG cc_start: 0.6957 (mmm-85) cc_final: 0.6381 (ttt-90) REVERT: B 493 ASP cc_start: 0.6960 (m-30) cc_final: 0.6538 (m-30) REVERT: B 527 GLU cc_start: 0.5799 (OUTLIER) cc_final: 0.5282 (tt0) REVERT: C 3 GLN cc_start: 0.7263 (mt0) cc_final: 0.6971 (mt0) REVERT: C 92 GLU cc_start: 0.7581 (pm20) cc_final: 0.6967 (mt-10) REVERT: C 97 LYS cc_start: 0.6602 (ttmm) cc_final: 0.6172 (mmmt) REVERT: C 122 MET cc_start: 0.7548 (mtm) cc_final: 0.7295 (mtp) REVERT: C 125 PRO cc_start: 0.7111 (Cg_exo) cc_final: 0.6632 (Cg_endo) REVERT: C 338 SER cc_start: 0.7944 (t) cc_final: 0.7614 (p) REVERT: C 344 MET cc_start: 0.7915 (mmt) cc_final: 0.7047 (mmm) REVERT: C 416 ARG cc_start: 0.7166 (mtm110) cc_final: 0.6519 (mtm180) REVERT: C 442 ASN cc_start: 0.8406 (m-40) cc_final: 0.8097 (m-40) REVERT: C 445 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6117 (tt0) REVERT: C 459 GLN cc_start: 0.6553 (mt0) cc_final: 0.6277 (mt0) REVERT: C 461 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: C 547 ARG cc_start: 0.6386 (mtp85) cc_final: 0.5996 (mtp180) REVERT: C 550 ARG cc_start: 0.7005 (ttm-80) cc_final: 0.6159 (mtm110) REVERT: C 552 ARG cc_start: 0.8034 (ptt90) cc_final: 0.7772 (ptt180) REVERT: C 562 TYR cc_start: 0.7747 (t80) cc_final: 0.7343 (t80) REVERT: D 26 ASP cc_start: 0.7601 (t0) cc_final: 0.7276 (t0) REVERT: D 52 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7342 (mm-30) REVERT: D 269 GLU cc_start: 0.6195 (tt0) cc_final: 0.5593 (mt-10) REVERT: D 305 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6531 (mtpp) REVERT: D 362 MET cc_start: 0.7561 (ttp) cc_final: 0.7039 (ttt) REVERT: D 406 GLU cc_start: 0.5928 (tp30) cc_final: 0.5363 (pm20) REVERT: D 437 GLN cc_start: 0.7761 (tt0) cc_final: 0.7472 (tt0) REVERT: D 444 SER cc_start: 0.7619 (p) cc_final: 0.7182 (m) REVERT: D 446 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7333 (mt) REVERT: D 461 LYS cc_start: 0.7164 (ttmm) cc_final: 0.6265 (mttt) REVERT: D 463 TYR cc_start: 0.7763 (t80) cc_final: 0.6751 (t80) REVERT: E 88 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7252 (mtt) REVERT: E 132 GLN cc_start: 0.7392 (tt0) cc_final: 0.7155 (tt0) REVERT: E 228 THR cc_start: 0.8434 (t) cc_final: 0.7881 (m) REVERT: E 302 GLU cc_start: 0.7117 (tt0) cc_final: 0.6906 (tt0) REVERT: E 305 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7721 (mtpp) REVERT: E 360 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6733 (mtt-85) REVERT: E 368 LYS cc_start: 0.6256 (OUTLIER) cc_final: 0.5702 (tppt) REVERT: E 410 ARG cc_start: 0.5483 (mtm-85) cc_final: 0.4329 (mmp80) REVERT: F 53 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6203 (pt0) REVERT: F 77 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6724 (pt0) REVERT: F 98 LYS cc_start: 0.7014 (mttt) cc_final: 0.6742 (mmtm) REVERT: F 109 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6327 (mm-30) REVERT: F 130 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7503 (t80) REVERT: F 207 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6184 (tm-30) REVERT: F 209 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6866 (mt-10) REVERT: F 210 ARG cc_start: 0.5884 (ttp80) cc_final: 0.5528 (ttp80) REVERT: F 280 ARG cc_start: 0.7478 (mtp85) cc_final: 0.7218 (mtt-85) REVERT: F 302 GLU cc_start: 0.7470 (tt0) cc_final: 0.6997 (tt0) REVERT: F 362 MET cc_start: 0.8384 (ttm) cc_final: 0.8042 (ttt) REVERT: F 452 LYS cc_start: 0.7063 (mmtp) cc_final: 0.6606 (mmtp) REVERT: G 9 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6349 (ptm) REVERT: G 47 MET cc_start: 0.5275 (mmm) cc_final: 0.4873 (ttm) REVERT: G 59 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.4590 (tp30) REVERT: G 146 ARG cc_start: 0.6792 (mmm-85) cc_final: 0.5795 (ttm-80) REVERT: G 149 LYS cc_start: 0.7244 (tptt) cc_final: 0.6979 (tptt) REVERT: G 200 LYS cc_start: 0.5120 (OUTLIER) cc_final: 0.4707 (mttt) REVERT: H 77 LEU cc_start: 0.4695 (mm) cc_final: 0.4156 (mt) REVERT: J 86 ARG cc_start: 0.4314 (mmp80) cc_final: 0.3408 (ttm-80) REVERT: J 112 LEU cc_start: 0.4498 (OUTLIER) cc_final: 0.4276 (mp) REVERT: J 184 GLN cc_start: 0.3671 (OUTLIER) cc_final: 0.2928 (tm-30) REVERT: K 102 LYS cc_start: 0.5256 (tptp) cc_final: 0.3866 (mmtt) REVERT: L 86 ARG cc_start: 0.4835 (mtt180) cc_final: 0.4574 (mtp180) REVERT: L 102 GLU cc_start: 0.5375 (mp0) cc_final: 0.4395 (tp30) REVERT: L 164 GLU cc_start: 0.5427 (tp30) cc_final: 0.4957 (mt-10) outliers start: 116 outliers final: 87 residues processed: 494 average time/residue: 0.5198 time to fit residues: 383.0338 Evaluate side-chains 514 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 408 time to evaluate : 3.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 184 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 5.9990 chunk 354 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 246 optimal weight: 3.9990 chunk 371 optimal weight: 7.9990 chunk 342 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 388 ASN F 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30052 Z= 0.316 Angle : 0.580 8.694 40716 Z= 0.301 Chirality : 0.046 0.254 4564 Planarity : 0.005 0.049 5331 Dihedral : 5.422 78.129 4214 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.67 % Allowed : 15.73 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3764 helix: 0.52 (0.13), residues: 1548 sheet: -0.76 (0.20), residues: 589 loop : -0.29 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 175 HIS 0.006 0.001 HIS D 375 PHE 0.019 0.002 PHE C 230 TYR 0.013 0.002 TYR D 283 ARG 0.005 0.001 ARG L 153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 410 time to evaluate : 3.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: A 53 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7105 (mm-30) REVERT: A 95 ARG cc_start: 0.6489 (tpt-90) cc_final: 0.5867 (tpt-90) REVERT: A 119 TRP cc_start: 0.8232 (OUTLIER) cc_final: 0.7175 (t-100) REVERT: A 154 ARG cc_start: 0.7022 (mtp85) cc_final: 0.6659 (mtp180) REVERT: A 169 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6840 (mt-10) REVERT: A 257 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7463 (mm-30) REVERT: A 340 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.5475 (mpp-170) REVERT: A 374 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6059 (tt0) REVERT: A 416 ARG cc_start: 0.7548 (mtm-85) cc_final: 0.6415 (mtp85) REVERT: A 478 ASP cc_start: 0.6428 (m-30) cc_final: 0.6141 (m-30) REVERT: A 481 ARG cc_start: 0.7091 (mtm-85) cc_final: 0.6403 (mmm160) REVERT: A 518 MET cc_start: 0.8296 (mtp) cc_final: 0.7993 (mtm) REVERT: A 541 GLN cc_start: 0.6305 (mt0) cc_final: 0.5683 (pt0) REVERT: A 550 ARG cc_start: 0.6854 (mtm-85) cc_final: 0.6584 (tpp-160) REVERT: A 557 GLU cc_start: 0.7241 (pm20) cc_final: 0.6417 (tp30) REVERT: B 128 GLU cc_start: 0.6569 (mm-30) cc_final: 0.6005 (tm-30) REVERT: B 129 VAL cc_start: 0.7713 (p) cc_final: 0.7212 (m) REVERT: B 154 ARG cc_start: 0.6588 (ptp90) cc_final: 0.6178 (ptt-90) REVERT: B 161 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6251 (mmtt) REVERT: B 180 GLU cc_start: 0.6853 (tt0) cc_final: 0.6347 (tt0) REVERT: B 197 ARG cc_start: 0.6626 (ttp80) cc_final: 0.6177 (ttp-110) REVERT: B 211 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7805 (tt) REVERT: B 340 ARG cc_start: 0.6878 (tpp-160) cc_final: 0.6547 (tpt-90) REVERT: B 384 VAL cc_start: 0.7912 (t) cc_final: 0.7610 (m) REVERT: B 397 GLN cc_start: 0.6793 (mm-40) cc_final: 0.6414 (tt0) REVERT: B 449 GLU cc_start: 0.6151 (mm-30) cc_final: 0.5396 (mt-10) REVERT: B 481 ARG cc_start: 0.6946 (mmm-85) cc_final: 0.6369 (ttt-90) REVERT: B 527 GLU cc_start: 0.5814 (OUTLIER) cc_final: 0.5266 (tt0) REVERT: C 3 GLN cc_start: 0.7336 (mt0) cc_final: 0.7058 (mt0) REVERT: C 92 GLU cc_start: 0.7522 (pm20) cc_final: 0.7095 (mt-10) REVERT: C 97 LYS cc_start: 0.6411 (ttmm) cc_final: 0.6067 (ttmt) REVERT: C 122 MET cc_start: 0.7529 (mtm) cc_final: 0.7289 (mtp) REVERT: C 125 PRO cc_start: 0.7112 (Cg_exo) cc_final: 0.6643 (Cg_endo) REVERT: C 338 SER cc_start: 0.7943 (t) cc_final: 0.7599 (p) REVERT: C 344 MET cc_start: 0.7914 (mmt) cc_final: 0.7127 (mmm) REVERT: C 416 ARG cc_start: 0.7164 (mtm110) cc_final: 0.6523 (mtm180) REVERT: C 442 ASN cc_start: 0.8411 (m-40) cc_final: 0.8099 (m-40) REVERT: C 459 GLN cc_start: 0.6542 (mt0) cc_final: 0.6281 (mt0) REVERT: C 460 ARG cc_start: 0.7031 (mtp180) cc_final: 0.6781 (mtm-85) REVERT: C 461 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: C 547 ARG cc_start: 0.6376 (mtp85) cc_final: 0.5985 (mtp180) REVERT: C 550 ARG cc_start: 0.6998 (ttm-80) cc_final: 0.6148 (mtm110) REVERT: C 552 ARG cc_start: 0.8029 (ptt90) cc_final: 0.7770 (ptt180) REVERT: C 562 TYR cc_start: 0.7768 (t80) cc_final: 0.7373 (t80) REVERT: D 26 ASP cc_start: 0.7654 (t0) cc_final: 0.7334 (t0) REVERT: D 52 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7343 (mm-30) REVERT: D 269 GLU cc_start: 0.6182 (tt0) cc_final: 0.5587 (mt-10) REVERT: D 305 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6534 (mtpp) REVERT: D 362 MET cc_start: 0.7557 (ttp) cc_final: 0.7066 (ttt) REVERT: D 406 GLU cc_start: 0.5884 (tp30) cc_final: 0.5343 (pm20) REVERT: D 437 GLN cc_start: 0.7762 (tt0) cc_final: 0.7473 (tt0) REVERT: D 444 SER cc_start: 0.7662 (p) cc_final: 0.7189 (m) REVERT: D 446 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7359 (mt) REVERT: D 461 LYS cc_start: 0.7168 (ttmm) cc_final: 0.6278 (mttt) REVERT: D 463 TYR cc_start: 0.7760 (t80) cc_final: 0.6780 (t80) REVERT: E 88 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7247 (mtt) REVERT: E 132 GLN cc_start: 0.7387 (tt0) cc_final: 0.7149 (tt0) REVERT: E 141 MET cc_start: 0.7782 (mtp) cc_final: 0.7505 (mmm) REVERT: E 302 GLU cc_start: 0.7152 (tt0) cc_final: 0.6936 (tt0) REVERT: E 305 LYS cc_start: 0.7980 (mtmm) cc_final: 0.7726 (mtpp) REVERT: E 360 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6739 (mtt-85) REVERT: E 368 LYS cc_start: 0.6260 (OUTLIER) cc_final: 0.5714 (tppt) REVERT: E 410 ARG cc_start: 0.5489 (mtm-85) cc_final: 0.4351 (mmp80) REVERT: F 53 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6220 (pt0) REVERT: F 77 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6758 (pt0) REVERT: F 98 LYS cc_start: 0.7038 (mttt) cc_final: 0.6750 (mmtm) REVERT: F 109 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6320 (mm-30) REVERT: F 130 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7494 (t80) REVERT: F 207 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6191 (tm-30) REVERT: F 209 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6854 (mt-10) REVERT: F 210 ARG cc_start: 0.5900 (ttp80) cc_final: 0.5553 (ttp80) REVERT: F 280 ARG cc_start: 0.7476 (mtp85) cc_final: 0.7227 (mtt-85) REVERT: F 302 GLU cc_start: 0.7469 (tt0) cc_final: 0.7000 (tt0) REVERT: F 362 MET cc_start: 0.8384 (ttm) cc_final: 0.8044 (ttt) REVERT: F 452 LYS cc_start: 0.7020 (mmtp) cc_final: 0.6569 (mmtp) REVERT: G 9 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.6354 (ptm) REVERT: G 47 MET cc_start: 0.5285 (mmm) cc_final: 0.4876 (ttm) REVERT: G 59 GLU cc_start: 0.5686 (OUTLIER) cc_final: 0.4589 (tp30) REVERT: G 146 ARG cc_start: 0.6870 (mmm-85) cc_final: 0.5946 (ttm110) REVERT: G 149 LYS cc_start: 0.7317 (tptt) cc_final: 0.7037 (tptt) REVERT: G 200 LYS cc_start: 0.5116 (OUTLIER) cc_final: 0.4695 (mttt) REVERT: H 77 LEU cc_start: 0.4799 (mm) cc_final: 0.4346 (mt) REVERT: J 86 ARG cc_start: 0.4318 (mmp80) cc_final: 0.3408 (ttm-80) REVERT: J 184 GLN cc_start: 0.3700 (OUTLIER) cc_final: 0.2895 (tm-30) REVERT: K 102 LYS cc_start: 0.5315 (tptp) cc_final: 0.3926 (mmtt) REVERT: L 86 ARG cc_start: 0.4845 (mtt180) cc_final: 0.4607 (mtp180) REVERT: L 164 GLU cc_start: 0.5456 (tp30) cc_final: 0.4965 (mt-10) outliers start: 113 outliers final: 91 residues processed: 488 average time/residue: 0.5046 time to fit residues: 363.0814 Evaluate side-chains 511 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 402 time to evaluate : 3.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 184 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 7.9990 chunk 315 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 272 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 82 optimal weight: 10.0000 chunk 296 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 304 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 571 GLN E 142 ASN F 388 ASN F 413 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.152942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.121022 restraints weight = 34533.972| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.72 r_work: 0.3024 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30052 Z= 0.244 Angle : 0.534 7.623 40716 Z= 0.277 Chirality : 0.044 0.236 4564 Planarity : 0.005 0.050 5331 Dihedral : 5.225 77.842 4214 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.50 % Allowed : 16.12 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3764 helix: 0.71 (0.13), residues: 1556 sheet: -0.73 (0.20), residues: 591 loop : -0.27 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 119 HIS 0.005 0.001 HIS D 375 PHE 0.020 0.002 PHE C 230 TYR 0.011 0.001 TYR F 463 ARG 0.007 0.000 ARG J 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8072.36 seconds wall clock time: 145 minutes 1.02 seconds (8701.02 seconds total)